bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanism of hcnA mRNA recognition in the Gac/Rsm signal transduction pathway of Pseudomonas fluorescens
Authors: Lapouge Karine , Sineva Elena , Lindell Magnus , Starke Katja , Baker Carol S. , Babitzke Paul , Haas Dieter 
Published: September 2007

SummaryIn the plant‐beneficial bacterium Pseudomonas fluorescens CHA0, the expression of antifungal exoproducts is controlled by the GacS/GacA two‐component system. Two RNA binding proteins (RsmA, RsmE) ensure effective translational repression of exoproduct mRNAs. At high cell population densities, GacA induces three small RNAs (RsmX, RsmY, RsmZ) which sequester both RsmA and RsmE, thereby relieving translational repression. Here we systematically analyse the features that allow the RNA binding proteins to interact strongly with the 5′ untranslated leader mRNA of the P. fluorescens hcnA gene (encoding hydrogen cyanide synthase subunit A). We obtained evidence for three major RsmA/RsmE recognition elements in the hcnA leader, based on directed mutagenesis, RsmE footprints and toeprints, and in vivo expression data. Two recognition elements were found in two stem‐loop structures whose existence in the 5′ leader region was confirmed by lead(II) cleavage analysis. The third recognition element, which overlapped the hcnA Shine–Dalgarno sequence, was postulated to adopt either an open conformation, which would favour ribosome binding, or a stem‐loop structure, which may form upon interaction with RsmA/RsmE and would inhibit access of ribosomes. Effective control of hcnA expression by the Gac/Rsm system appears to result from the combination of the three appropriately spaced recognition elements.
Pho85, a multifunctional cyclin‐dependent protein kinase in budding yeast
Authors: Huang Dongqing , Friesen Helena , Andrews Brenda 
Published: September 2007

SummaryPho85 is a multifunctional cyclin‐dependent kinase (Cdk) inSaccharomyces cerevisiaethat has emerged as an important model for the role of Cdks in both cell cycle control and other processes. Pho85 is targeted to its substrates by 10 different cyclins or Pcls. Three of these Pcls have specific roles in G1 phase of the cell cycle, both in regulating G1‐specific gene expression and in controlling polarized growth. Many known substrates of the G1 forms of Pho85 are also phosphorylated by the homologous Cdk Cln–Cdc28, suggesting parallel or overlapping roles. Most of the remaining Pcls function in signalling: Pho85 is generally active when environmental conditions are satisfactory, phosphorylating proteins involved in transcription and other regulatory events to keep the stress response and inappropriate activities turned off. Recently, genetic screens for synthetic lethality and synthetic dosage lethality, and proteomic screens forin vitroPho85 substrates, have revealed more details about how Pho85 functions to regulate a variety of cellular processes.
Microarray analysis of Mu transposition in Salmonella enterica, serovar Typhimurium: transposon exclusion by high‐density DNA binding proteins
Authors: Manna Dipankar , Porwollik Steffen , McClelland Michael , Tan Ruimin , Higgins N. Patrick 
Published: September 2007

SummaryAll organisms contain transposons with the potential to disrupt and rearrange genes. Despite the presence of these destabilizing sequences, some genomes show remarkable stability over evolutionary time. Do bacteria defend the genome against disruption by transposons? Phage Mu replicates by transposition and virtually all genes are potential insertion targets. To test whether bacteria limit Mu transposition to specific parts of the chromosome, DNA arrays of Salmonella enterica were used to quantitatively measure target site preference and compare the data with Escherichia coli. Essential genes were as susceptible to transposon disruption as non‐essential ones in both organisms, but the correlation of transposition hot spots among homologous genes was poor. Genes in highly transcribed operons were insulated from transposon mutagenesis in both organisms. A 10 kb cold spot on the pSLT plasmid was near parS, a site to which the ParB protein binds and spreads along DNA. Deleting ParB erased the plasmid cold spot, and an ectopic parS site placed in the Salmonella chromosome created a new cold spot in the presence of ParB. Our data show that competition between cellular proteins and transposition proteins on plasmids and the chromosome is a dominant factor controlling the genetic footprint of transposons in living cells.
Gradual activation of the response regulator DegU controls serial expression of genes for flagellum formation and biofilm formation in Bacillus subtilis
Authors: Kobayashi Kazuo 
Published: September 2007

SummaryIn natural environments, bacteria fluctuate between growth as motile cells and growth as sessile, biofilm‐forming cells. However, what controls the transition between these two‐growth modes in Bacillus subtilis is not well understood yet. The degU mutation prevents both flagellum formation and biofilm formation, suggesting that one of the transition mechanisms may underlie regulation of the DegU activity. The expression profiles of DegU‐regulated genes differed; flagellar genes and several unknown genes were expressed during the exponential phase, whereas other genes were induced in the stationary phase. The degS mutation did not affect transcription of the flgB‐sigD operon, but reduced transcription of σD‐dependent flagellar genes, degU and other DegU‐regulated genes. In addition, the degQ mutation did not affect transcription of flagellar genes but reduce transcription of other DegU‐regulated genes. Purified DegQ protein stimulated phosphotransfer from phospho‐DegS to DegU in vitro. Moreover, DegU binds the promoter region of flgB with a high affinity, whereas DegU binds to the promoter regions of other DegU‐regulated genes with a low affinity and in a DegS‐dependent manner. Taken together, we propose that a gradual increase in DegU and phospho‐DegU levels induces a transition from growth as motile cells to growth as sessile, biofilm‐forming cells.
Mutational analysis reveals Escherichia coli oriC interacts with both DnaA‐ATP and DnaA‐ADP during pre‐RC assembly
Authors: Grimwade Julia E. , Torgue Julien J.‐C. , McGarry Kevin C. , Rozgaja Tanya , Enloe Sareena T. , Leonard Alan C. 
Published: September 2007

SummaryPrior to initiating DNA synthesis, Escherichia coli oriC switches from ORC, comprising initiator DnaA bound at three high‐affinity sites, to pre‐RC, when additional DnaA molecules interact with low‐affinity sites. Two types of low‐affinity sites exist: R boxes that bind DnaA‐ATP and DnaA‐ADP with equal affinity, and I‐sites with a three‐ to fourfold preference for DnaA‐ATP. To assess the regulatory role of weak DnaA interactions during pre‐RC assembly in vivo, we compared the behaviour of plasmid‐borne wild‐type oriC with mutants having an increased or decreased number of DnaA‐ATP discriminatory I‐sites. Increasing the number of discriminatory sites by replacing R5M with I2 inactivated extrachromosomal oriC function. Mutants with no discriminatory sites perturbed host growth and rapidly replaced wild‐type chromosomal oriC, but normal function returned if one I‐site was restored at either the I2, I3 or R5M position. These observations are consistent with assembly of E. coli pre‐RC in vivo from mixtures of DnaA‐ATP and DnaA‐ADP, with I‐site interactions coupling pre‐RC assembly to DnaA‐ATP levels.
Chaperones specific for the membrane‐bound [NiFe]‐hydrogenase interact with the Tat signal peptide of the small subunit precursor in Ralstonia eutropha H16
Authors: Schubert Torsten , Lenz Oliver , Krause Eberhard , Volkmer Rudolf , Friedrich Bärbel 
Published: September 2007

SummaryPeriplasmic membrane‐bound [NiFe]‐hydrogenases undergo a complex maturation pathway, including cofactor incorporation, subunit assembly, and finally twin‐arginine‐dependent membrane translocation (Tat). In this study, the role of the two accessory proteins HoxO and HoxQ in the maturation of the membrane‐bound [NiFe]‐hydrogenase (MBH) of Ralstonia eutropha H16 was investigated. MBH activity was absent in soluble as well as membrane fractions of cells with deletions in the respective genes. The absence of HoxO and HoxQ led to degradation of the small subunit precursor (preHoxK) of the MBH. The two accessory proteins directly interacted with preHoxK prior to assembly of active MBH dimer in the cytoplasm. MBH mutants with modified Tat signal peptides were disrupted in preHoxK/HoxO/HoxQ complex formation. Isolated HoxO and HoxQ proteins formed a complex in vitro with the chemically synthesized HoxK Tat signal peptide. Two functions of the two chaperones are discussed: (i) protection of the Fe–S cluster containing HoxK subunit under oxygenic conditions, and (ii) avoidance of HoxK export prior to dimerization with the large MBH subunit HoxG.
Radio galaxies in the 2SLAQ Luminous Red Galaxy Survey – I. The evolution of low-power radio galaxies to z∼ 0.7
Authors: Sadler Elaine M. , Cannon Russell D. , Mauch Tom , Hancock Paul J. , Wake David A. , Ross Nic , Croom Scott M. , Drinkwater Michael J. , Edge Alastair C. , Eisenstein Daniel , Hopkins Andrew M. , Johnston Helen M. , Nichol Robert , Pimbblet Kevin A. , De Propris Roberto , Roseboom Isaac G. , Schneider Donald P. , Shanks Tom 
Published: September 2007

Abstract
We have combined optical data from the 2dF-SDSS (Sloan Digital Sky Survey) LRG (Luminous Red Galaxy) and QSO (quasi-stellar object) (2SLAQ) redshift survey with radio measurements from the 1.4 GHz VLA (Very Large Array) FIRST (Faint Images of the Radio Sky at Twenty-cm) and NVSS (NRAO VLA Sky Survey) surveys to identify a volume-limited sample of 391 radio galaxies at redshift 0.4 &lt; z &lt; 0.7. By determining an accurate radio luminosity function for luminous early-type galaxies in this redshift range, we can investigate the cosmic evolution of the radio-galaxy population over a wide range in radio luminosity.
The low-power radio galaxies in our LRG sample (those with 1.4 GHz radio luminosities in the range 1024 to 1025 W Hz−1, corresponding to Fanaroff–Riley I (FR I) radio galaxies in the local Universe) undergo significant cosmic evolution over the redshift range 0 &lt; z &lt; 0.7, consistent with pure luminosity evolution of the form (1 +z)k, where k= 2.0 ± 0.3. Our results appear to rule out (at the 6–7σ level) models in which low-power radio galaxies undergo no cosmic evolution. The most powerful radio galaxies in our sample (with radio luminosities above 1026 W Hz−1) may undergo more rapid evolution over the same redshift range.
The evolution seen in the low-power radio-galaxy population implies that the total energy input into massive early-type galaxies from active galactic nucleus (AGN) heating increases with redshift, and was at least 50 per cent higher at z∼ 0.55 (the median redshift of the 2SLAQ LRG sample) than in the local universe.
Capture of membrane components via trogocytosis occurs in vivo during both dendritic cells and target cells encounter by CD8+ T cells
Authors: Riond J. , Elhmouzi J. , Hudrisier D. , Gairin J. E. 
Published: September 2007

AbstractCytotoxic T lymphocytes recently stimulated by antigen‐presenting cells (APC) display major histocompatibility class (MHC) I and II molecules inherited from APC. We have previously reported that, in vitro, transfer of MHC molecules and several other proteins occurs through trogocytosis, i.e. the active acquisition of target cell membrane fragments by T lymphocytes. Here, using the model of viral antigen LCMVgp33‐41 recognition in transgenic P14 mice, we show that CD8+ T cells perform trogocytosis in vivo, as detected by the capture of biotin‐ or fluorescence‐labeled components of the APC surface. Trogocytosis occurs during interactions of CD8+ T cells with at least two kinds of cells: target cells and dendritic cells (DC). In lymph nodes, CD8+ T cells having performed trogocytosis with DC express the CD69 activation marker indicating that trogocytosis detects recently activated cells. Taken together, our findings suggest that trogocytosis may be a new in vivo marker of the recent interaction between a CD8+ T cell and its cellular partners or targets.
Late‐glacial and post‐glacial deposition in a large, low relief, epicontinental basin: the northern Baltic Sea
Authors: VIRTASALO JOONAS J. , KOTILAINEN AARNO T. , RÄSÄNEN MATTI E. , OJALA ANTTI E. K. 
Published: September 2007

AbstractThis paper presents a model of late‐glacial and post‐glacial deposition for the late‐Neogene sedimentary succession of the Archipelago Sea in the northern Baltic Sea. Four genetically related facies associations are described: (i) an ice‐proximal, acoustically stratified draped unit of glaciolacustrine rhythmites; (ii) an onlapping basin‐fill unit of rotated rhythmite clasts in an acoustically transparent to chaotic matrix interpreted as debris‐flow deposits; (iii) an ice‐distal, acoustically stratified to transparent, draped unit of post‐glacial lacustrine, weakly laminated to homogeneous deposits; and (iv) an acoustically stratified to transparent unit of brackish‐water, organic‐rich sediment drifts. The debris‐flow deposits of the unit 2 pass laterally into slide scars that truncate the unit 1; they are interpreted to result from a time interval of intense seismic activity due to bedrock stress release shortly after deglaciation of the area. Ice‐berg scouring and gravitational failure of oversteepened depositional slopes may also have contributed to the debris‐flow deposition. Comparisons to other late‐Neogene glaciated basins, such as the Hudson Bay or glacial lakes formed along the Laurentide ice sheet, suggest that the Archipelago Sea succession may record development typical for the deglaciation phase of large, low relief, epicontinental basins. The Carboniferous–Permian glacigenic Dwyka Formation in South Africa may provide an ancient analogue for the studied succession. Chronological control for the studied sediments is provided by the independent palaeomagnetic and AMS‐14C dating methods. In order to facilitate dating of the organic‐poor early post‐glacial deposits of the northern Baltic Sea, the 10 000 year long Lake Nautajärvi palaeomagnetic reference chronology (Ojala & Saarinen, 2002) is extended by 1200 years.
Spherical and columnar, septarian, 18O‐depleted, calcite concretions from Middle–Upper Permian lacustrine siltstones in northern Mozambique: evidence for very early diagenesis and multiple fluids
Authors: MELEZHIK VICTOR A. , FALLICK ANTHONY E. , SMITH RICHARD A. , ROSSE DANTA M. 
Published: September 2007

AbstractCalcite septarian concretions from the Permian Beaufort Group in the Maniamba Graben (NW Mozambique) allow controls on the composition and nature of diagenetic fluids to be investigated. The concretions formed in lacustrine siltstones, where they occur in spherical (1 to 70 cm in diameter) and columnar (up to 50 cm long) forms within three closely spaced, discrete beds totalling 2·5 m in thickness. Cementation began at an early stage of diagenesis and entrapped non‐compacted burrows and calcified plant roots. The cylindrical concretions overgrew calcified vertical plant roots, which experienced shrinkage cracking after entrapment. Two generations of concretionary body cement and two generations of septarian crack infill are distinguished. The early generation in both cases is a low‐Mn, Mg‐rich calcite, whereas the later generation is a low‐Mg, Mn‐rich calcite. The change in chemistry is broadly consistent with a time (burial)‐related transition from oxic to sub‐oxic/anoxic conditions close to the sediment–water interface. Geochemical features of all types of cement were controlled by the sulphate‐poor environment and by the absence of bacterial sulphate reduction. All types of cement present have δ13C ranging between 0‰ and −15‰(Vienna Peedee Belemnite, V‐PDB), and highly variable and highly depleted δ18O (down to 14‰ Vienna Standard Mean Ocean Water, V‐SMOW). The late generation of cement is most depleted in both 13C and 18O. The geochemical and isotopic patterns are best explained by interaction between surface oxic waters, pore waters and underground, 18O‐depleted, reducing, ice‐meltwaters accumulated in the underlying coal‐bearing sediments during the Permian deglaciation. The invariant δ13C distribution across core‐to‐rim transects for each individual concretion is consistent with rapid lithification and involvement of a limited range of carbon sources derived via oxidation of buried plant material and from dissolved clastic carbonates. Syneresis of the cement during an advanced stage of lithification at early diagenesis is considered to be the cause of development of the septarian cracks. After cracking, the concretions retained a small volume of porosity, allowing infiltration of anoxic, Ba‐bearing fluids, resulting in the formation of barite. The results obtained contribute to a better understanding of diagenetic processes at the shallow burial depths occurring in rift‐bound, lacustrine depositional systems.
Submarine mass‐transport facies: new perspectives on flow processes from cores on the eastern North American margin
Authors: TRIPSANAS EFTHYMIOS K. , PIPER DAVID J. W. , JENNER KIMBERLEY A. , BRYANT WILLIAM R. 
Published: September 2007

AbstractNo comprehensive scheme yet exists to describe the depositional products of submarine sediment failures at the scale of piston cores, resulting in misinterpretation of failure deposits and overuse of the genetic term ‘debris flow’. Ninety‐nine sediment cores (0·5 to 20 m in length), from offshore eastern Canada and the Gulf of Mexico, are used to propose a descriptive sedimentary facies scheme with genetic implications for mass‐transport deposits. Seven facies are distinguished: (i) allochthonous stratified sediment; (ii) distorted stratified sediment; (iii) clast‐supported hard‐mud‐clast conglomerate; (iv) matrix‐supported mud‐clast conglomerate; (v) thin mud‐clast conglomerate (<0·8 m thick); (vi) diamicton; and (vii) sorted sand‐gravel deposits (≥0·05 m thick).Seven genetic types of deposits are recognized. (i) Slumping of coherent sediment blocks (facies I). (ii) Slump and slide deposits (facies I and II). (iii) Debris‐avalanche deposits (hard sediment of facies I and II overlain by facies III). (iv) Low‐viscosity or large‐scale, high‐viscosity, cohesive debris flow deposits (facies IV, may have I, II, and III). (v) Very low‐viscosity debris flow deposits (facies V). (vi) Cohesionless debris flow deposits (facies VI). (vii) High‐density turbidity currents (facies VII). Vertical transitions between the genetic types were analysed by Markov chain analysis.Although sedimentological transitions are inferred between deposits of slides and cohesive debris flows, their spatial distribution indicates that a cohesive debris flow forms principally in the initial stages of a sediment failure, suggesting that transformation depends mostly on the strength of the sediments. A genetic link is suggested for cohesionless debris flow deposits, which originate from the disintegration of sandy sediment on the upper continental slope, and the closely related turbidity current deposits. Debris avalanches are common in sedimentary marine environments with steep slopes (>10°). In many cases, geometrical and seismic characteristics of debris avalanche, slide and debris flow are similar, requiring core data to verify transport process.
Morphological characterization of cluster microforms
Authors: STROM K. B. , PAPANICOLAOU A. N. 
Published: September 2007

AbstractA field study was conducted on two mountain streams in the Cascade Mountains of Washington State on the morphological characterization of cluster microforms. Morphological characterization of clusters is presented in terms of: (i) cluster shape; (ii) cluster geometric properties; and (iii) the spatial arrangement of clusters in the horizontal plane. Clusters were differentiated from other microtopography features such as reticulate structures and transverse ribs, and identified clusters were categorized by shape as being of pebble, line, comet, heap or ring type. The complex spatial arrangement of clusters at the sites was characterized by using a two‐dimensional correlation function, which allowed for measurement of the average cluster‐spacing properties. For the rivers examined, pebble‐shaped clusters were the most frequently observed cluster shape. Cluster geometric properties were found to be controlled by particles of the largest size fraction in the bed and the projected frontal width of the cluster – with cluster length being linearly related to cluster width for cluster width‐to‐height ratios <3·5. Results of the cluster‐spacing analysis suggest that cluster spacing increases with cluster size and decreases with local slope. Application of this principle to the available spacing data shows that cluster spacing λ scales with the ratio of S/d0 such that λS/d0 = constant, where S is the local slope and d0 the diameter of the largest particle in the cluster.
PRECLINICAL STUDY: Age‐dependent differences in sensitivity and sensitization to cannabinoids and ‘club drugs’ in male adolescent and adult rats
Authors: Wiley Jenny L. , Evans Rhys L. , Grainger Darren B. , Nicholson Katherine L. 
Published: September 2007

ABSTRACTLifelong substance abuse is often initiated during adolescence; yet, most pre‐clinical research in this area has been conducted in adult animals. Substantial evidence exists that the brain development that continues throughout adolescence may result in pharmacological responses that differ in a crucial manner from those of adults. The goal of this study was to evaluate age differences in motor activity following acute and repeated administration of drugs that are commonly abused by adolescents, including cocaine, Δ9‐tetrahydrocannabinol (Δ9‐THC), and the club drugs, ketamine and 3,4‐methylenedioxymethamphetamine (MDMA). Adolescent and adult male rats were injected once daily with saline or with a dose of one of the test drugs for two 5‐day dosing periods, separated by a 2‐day drug holiday during which they remained in their home cages. Following each injection, rats were placed in a locomotor chamber for a 20‐minute session. The potencies of cocaine, ketamine and MDMA for producing motor stimulation were less in male adolescents than in male adults. Furthermore, sensitization to the club drug, ketamine, developed after repeated dosing in adults, but not adolescents. In contrast, adolescents were initially more sensitive to the stimulatory effects of low doses of Δ9‐THC than were adults, although rapid tolerance occurred. These results suggest that adolescents are less sensitive to the acute and repeated stimulant effects of some, but not all, of the drugs that are preferentially abused by this age group. This differential sensitivity may contribute to the different patterns of use that have been noted in adolescent versus adult drug abusers.