bluuebunny/crossref_metadata_2025_split huggingface dataset:
RcsCDB His‐Asp phosphorelay system negatively regulates the flhDC operon in Escherichia coli
Authors: Francez‐Charlot Anne , Laugel Bruno , Van Gemert Alice , Dubarry Nelly , Wiorowski Florent , Castanié‐Cornet Marie‐Pierre , Gutierrez Claude , Cam Kaymeuang 
Published: July 2003

SummaryThe genes involved in flagellum synthesis, motility and chemotaxis in Escherichia coli are expressed in a hierarchical fashion. At the top of the hierarchy lies the master regulator FlhDC, required for the expression of the whole set of genes. The operon flhDC is controlled by numerous regulators including H‐NS, CRP, EnvZ/OmpR, QseBC and LrhA. In the present work, we report that the flhDC operon is also negatively regulated by the His‐Asp phosphorelay system RcsCDB. The regulation is potentiated by the RcsB cofactor RcsA. Genetic analysis indicates that an RcsAB box, located downstream of the promoter, is required for the regulation. The binding of RcsB and RcsA to this site was demonstrated by gel retardation and DNase I protection assays. In addition, mutation analysis suggests that RcsA‐specific determinants lie in the right part of the ‘RcsAB box’.
DnaA Protein of Escherichia coli: oligomerization at the E. coli chromosomal origin is required for initiation and involves specific N‐terminal amino acids
Authors: Simmons Lyle A. , Felczak Magdalena , Kaguni Jon M. 
Published: July 2003

SummaryIterated DnaA box sequences within the replication origins of bacteria and prokaryotic plasmids are recognized by the replication initiator, DnaA protein. At the E. coli chromosomal origin, oriC, DnaA is speculated to oligomerize to initiate DNA replication. We developed an assay of oligomer formation at oriC that relies on complementation between two dnaA alleles that are inactive by themselves. One allele is dnaA46; its inactivity at the non‐permissive temperature is due to a specific defect in ATP binding. The second allele, T435K, does not support DNA replication because of its inability to bind to DnaA box sequences within oriC. We show that the T435K allele can complement the dnaA46(Ts) allele. The results support a model of oligomer formation in which DnaA box sequences of oriC are bound by DnaA46 to which T435K then binds to form an active complex. Relying on this assay, leucine 5, tryptophan 6 and cysteine 9 in a predicted alpha helix were identified that, when altered, interfere with oligomer formation. Glutamine 8 is additionally needed for oligomer formation on an oriC‐containing plasmid, suggesting that the structure of the DnaA‐oriC complex at the chromosomal oriC locus is similar but not identical to that assembled on a plasmid. Other evidence suggests that proline 28 of DnaA is involved in the recruitment of DnaB to oriC. These results provide direct evidence that DnaA oligomerization at oriC is required for initiation to occur.
Spatial and temporal organization of replicating Escherichia coli chromosomes
Authors: Lau Ivy F. , Filipe Sergio R. , Søballe Britta , Økstad Ole‐Andreas , Barre Francois‐Xavier , Sherratt David J. 
Published: July 2003

SummaryThe positions of DNA regions close to the chromosome replication origin and terminus in growing cells of Escherichia coli have been visualized simultaneously, using new widely applicable reagents. Furthermore, the positions of these regions with respect to a replication factory‐associated protein have been analysed. Time‐lapse analysis has allowed the fate of origins, termini and the FtsZ ring to be followed in a lineage‐specific manner during the formation of microcolonies. These experiments reveal new aspects of the E. coli cell cycle and demonstrate that the replication terminus region is frequently located asymmetrically, on the new pole side of mid‐cell. This asymmetry could provide a mechanism by which the chromosome segregation protein FtsK, located at the division septum, can act directionally to ensure that the septal region is free of DNA before the completion of cell division.
Consumer‐resource stoichiometry in detritus‐based streams
Authors: Cross Wyatt F. , Benstead Jonathan P. , Rosemond Amy D. , Bruce Wallace J. 
Published: July 2003

AbstractStoichiometric relationships between consumers and resources in detritus‐based ecosystems have received little attention, despite the importance of detritus in most food webs. We analysed carbon (C), nitrogen (N), and phosphorus (P) content of invertebrate consumers, and basal food resources in two forested headwater streams (one reference and the other nutrient‐enriched). We found large elemental imbalances between consumers and food resources compared with living plant‐based systems, particularly in regard to P content, which were reduced with enrichment. Enrichment significantly increased nutrient content of food resources (consistent with uptake of N and P by detritus‐associated microbes). P content of some invertebrates also increased in the enriched vs. reference stream, suggesting deviation from strict homeostasis. Nutrient content varied significantly among invertebrate functional feeding groups, orders and, to some extent, size classes. Future application of stoichiometric theory to detritus‐based systems should consider the potential for relatively large consumer‐resource elemental imbalances and P storage by insect consumers.
Reconsidering diversity–productivity relationships: directness of productivity estimates matters
Authors: Groner Elli , Novoplansky Ariel 
Published: July 2003

AbstractDespite extensive research efforts, the controversy over diversity–productivity (D–P) patterns in natural communities still looms large. Recent meta‐analyses suggest that unimodal D–P relationships tend to pre‐dominate in plant studies, while positively linear relationships are more common in animal studies. These patterns, however, are based on studies in which productivity is estimated either directly, based on the biomass or energy of the studied organisms, or indirectly, according to the productivity of lower trophic levels, and various surrogates. Our analysis shows that the distribution of D–P patterns is sensitive to the directness of productivity estimates in animal studies but not in plant studies. Analysis of D–P patterns should be based on direct productivity estimates of the studied organisms, especially in comparative meta‐analyses of communities from multiple trophic levels, where productivity is often affected nonlinearly by indirect factors or when complex feedback interactions are expected between productivity and diversity.
Scale‐dependent interactions between intrinsic and extrinsic processes reduce variability in protist populations
Authors: Orland Mary C. 
Published: July 2003

AbstractInteractions between intrinsic processes and extrinsic fluctuations can positively impact population persistence in ways often not predicted by classic ecological models. These interactions only arise when the intrinsic and extrinsic processes operate on the proper relative scales in time or space. Both metapopulation theory and resonance/attenuation theory suggest that interactions which lower population variability will occur when the intrinsic and extrinsic process occur on similar time scales. I performed an aquatic protist microcosm experiment to investigate how the relative frequencies of extrinsic density perturbations and intrinsic resource pulses impacted population variability. Population variability was lowest in the treatments of intermediate frequency, in which the extrinsic fluctuations and intrinsic processes were on the same time scale. This result is consistent with general theoretical predictions, and empirically documents the importance of considering scale in interactions between intrinsic and extrinsic processes that positively impact population persistence.
Neighbour‐regulated mortality: the influence of positive and negative density dependence on tree populations in species‐rich tropical forests
Authors: Peters Halton A. 
Published: July 2003

AbstractDensity‐dependent mortality has long been posited as a possible mechanism for the regulation of tropical forest tree density. Despite numerous experimental and phenomenological investigations, the extent to which such mechanisms operate in tropical forests remains unresolved because the demographical signature of density dependence has rarely been found in extensive investigations of established trees. This study used an individual‐based demographical approach to investigate the role of conspecific and heterospecific neighbourhood crowding on tree mortality in a Panamanian and a Malayan tropical forest. More than 80% of the species investigated at each site were found to exhibit density‐dependent mortality. Furthermore, most of these species showed patterns of mortality consistent with the Janzen–Connell hypothesis and the rarely explored hypothesis of species herd protection. This study presents some of the first evidence of species herd protection operating in tree communities.
Biological invasions drive size increases in marine and estuarine invertebrates
Authors: Grosholz Edwin D. , Ruiz Gregory M. 
Published: July 2003

AbstractEcologists have long been fascinated by the morphological changes that species frequently undergo when introduced into new regions. In this study an unusual pattern of size change associated with the invasion of 19 species of marine and estuarine invertebrates is reported. The results show that the majority of species are significantly larger in the introduced range compared with the native range with little evidence for any decrease in size following invasion. This invasion‐driven increase in body size sharply contrasts with the pattern observed in many other taxa including plants, mammals and lizards, where invaders frequently exhibit post‐invasion decreases and increases in size. These size changes were not influenced by differences in latitude, sample size or length of time since invasion. Although several mechanisms, may explain the results, none have been demonstrated.
Herbivores and the success of exotic plants: a phylogenetically controlled experiment
Authors: Agrawal Anurag A. , Kotanen Peter M. 
Published: July 2003

AbstractIn a field experiment with 30 locally occurring old‐field plant species grown in a common garden, we found that non‐native plants suffer levels of attack (leaf herbivory) equal to or greater than levels suffered by congeneric native plants. This phylogenetically controlled analysis is in striking contrast to the recent findings from surveys of exotic organisms, and suggests that even if ‘enemy release’ does accompany the invasion process, this may not be an important mechanism of invasion, particularly for plants with close relatives in the recipient flora.
U/Th‐rich bitumen in Archean granites and Palaeoproterozoic metasediments, Rum Jungle Mineral Field, Australia: implications for mineralizing fluids
Authors: McCready A. J. , Stumpfl E. F. , Melcher F. 
Published: July 2003

AbstractUranium/thorium (U/Th)‐rich bitumen has been discovered within both Palaeoproterozoic black pelites and the Archean granitic basement of the Rum Jungle Mineral Field, Northern Territory, Australia. Granite‐hosted bitumen occurs as small (up to 400‐µm diameter) discrete individual nodules, which exhibit many morphological similarities to those observed in Phanerozoic siliciclastic rocks. Thorium, the dominant radioelement, occurs primarily as a hydrated Th–Y–Si–P phase. Uranium‐rich inclusions are rare, and correspond to a hydrated U–Th–Y–Si–P phase, identified as coffinite–thorogummite. Metasediment‐hosted bitumen is more variable in morphology, occurring as massive (<2 cm in width) veins that cross‐cut all foliations, as discrete individual nodules or as elongate seams (up to 500 µm in length), interpreted to represent a series of coalesced individual nodules. In all examples, uranium, the dominant radioelement in the metasediment‐hosted bitumen, is present as Th‐poor uraninite, with variable Y2O3contents (up to 3.21 wt.%).Raman investigation of all types of bitumen indicates that it is a poorly organized carbonaceous matter, which has not been subjected to metamorphism. Consequently, a post‐metamorphic timing for hydrocarbon emplacement can be inferred and a magmatic origin can be precluded.Potential source rocks for the bitumen are black shales of the Whites Formation (up to 8 wt.% total organic carbon (TOC)) and the Koolpin Formation (approximately 13 wt.% TOC). Post‐metamorphic sericitization of rocks within the Whites Formation is accompanied by a near‐complete removal of organic matter. Alteration was possibly the catalyst for hydrocarbon generation.The Th–Y–Si–P phase within the granite‐hosted nodules is interpreted to be the result of the alteration of antecedent monazite. During this alteration, U, LREE and P were fractionated and removed, while Th, Y and Si remained immobile, and recombined to form a hydrated Th–Y–Si phase. This pervasive alteration within the basement U/Th‐rich granites is proposed as a genetic model for the formation of uranium deposits in the Rum Jungle Mineral Field and possibly unconformity associated uranium deposits on a global scale.
Geothermal fluids circulation at Caldas do Moledo area, Northern Portugal: geochemical and isotopic signatures
Authors: Marques J. M. , Marques J. Espinha , Carreira P. M. , Graça R. C. , Aires‐Barros L. , Carvalho J. M. , Chaminé H. I. , Borges F. S. 
Published: July 2003

AbstractA hydrogeological conceptual model of the Caldas do Moledo geothermal site is proposed that shows mixing between geothermal waters and local shallow groundwaters. Stable isotope values of Caldas do Moledo geothermal waters indicate recharge areas located at relatively high altitudes (850–1250 m a.s.l.). The NW–SE Vigo–Régua shear zone plays an important role in fluid recharge and circulation towards the NNE–SSW Régua–Verin fault system, forming a path for ascent of geothermal fluids. The apparent 14C age of geothermal fluids (15.66 ± 2.86 ka BP) was estimated in the total dissolved inorganic carbon (TDIC). Geothermometer calculations indicate that, assuming a conductive temperature gradient of 32°C per kilometer for northern Portugal, the maximum depth of circulation is roughly 1.8 ± 0.4 km. The K, Ca and SO4 concentrations found in some Caldas do Moledo geothermal spring waters show mixing between deep geothermal and shallow groundwater systems. Local shallow groundwaters showing the highest SO4 concentrations were found at low elevation areas, originating from fertilisers and pesticides applied to the Port wine vineyards in the Douro River valley. Geothermal waters from boreholes AC1 and AC2 do not show evidences of direct pollution from the spreading of such agrochemicals.
Abnormally pressured beds as barriers to diffusive solute transport in sedimentary basins
Authors: Wilson Alicia M. , Fenstemaker Thomas , Sharp John M. 
Published: July 2003

AbstractDiffusion can drive significant solute transport over millions of years, but ancient brines and large salinity gradients are still observed in deep sedimentary basins. Fluid flow within abnormally pressured beds may prevent diffusive transfer over geologically significant periods, if the abnormally pressured bed is surrounded by normally pressured beds. Analytic solutions based on sediment loading and unloading demonstrate that this effect should be considered in beds with a compressibility exceeding 10−8 Pa−1, with a thickness of 100 m or more, or a sedimentation rate exceeding 10−5 m year−1.Conditions favourable for our model of abnormally pressured beds appear common in sedimentary basins. Large salinity gradients associated with clay beds have previously been attributed to membrane effects, but flow patterns associated with abnormally pressured beds appear more robust in the presence of heterogeneity and discontinuities than membrane effects. Calculations suggest that thick underpressured shales in the Alberta basin may have allowed ancient evaporatively concentrated brines to be preserved beneath a vigorous topography‐driven flow system over the last 60 My. In the Illinois basin, drained overpressured beds may have limited solute transport across the New Albany shale until approximately 250 Ma. It is unlikely, however, that overpressures could have persisted long enough to explain concentration gradients observed in the modern basin. These gradients may instead reflect relatively recent halite dissolution above the New Albany shale.
Geothermometry and geobarometry of overpressured environments in Qiongdongnan Basin, South China Sea*
Authors: Chen Honghan , Wang Jiahao , Xie Yuhong , Wang Zhenfeng 
Published: July 2003

AbstractWe demonstrate the use of PVT fluid inclusion modelling in the calculation of palaeofluid formation pressures, using samples from the YC21‐1‐1 and YC21‐1‐4 wells in the YC21‐1 structural closure, Qiongdongnan Basin, South China Sea. Homogenisation temperatures and gas/liquid ratios were measured in aqueous fluid inclusions, and associated light hydrocarbon/CO2‐bearing inclusions, and their compositions were determined using a crushing technique. The vtflinc software was used to construct P–T phase diagrams that enabled derivation of the minimum trapping pressure for each order of fluid inclusion. Through the projection of average homogenisation temperatures (155, 185.5 and 204.5°C) for three orders of fluid inclusion on the thermal‐burial history diagram of the Oligocene Yacheng and Lingshui formations, their trapping times were constrained at 4.3, 2.1 and 1.8 Ma, respectively. The formation pressure coefficient, the ratio of fluid pressure/hydrostatic pressure established by PVT modelling coupled with DST data, demonstrates that one and a half cycles of pressure increase–discharge developed in the Yacheng and Lingshui formations for about 4.3 Ma. In comparison, the residual formation pressure determined by 2D numerical modelling in the centre of LeDong depression shows two and a half pressure increase–discharge cycles for about 28 Ma. The two different methods suggest that a high fluid potential in the Oligocene reservoir of the YC21‐1 structure developed at two critical stages for regional oil and natural gas migration and accumulation (5.8 and 2.0 Ma, respectively). Natural gas exploration in this area is therefore not advisable.
Book Reviews
Authors: Fiedler Peggy L. 
Published: July 2003

Since the beginning of my tenure as associate editor for book reviews, I have received a great many books. This wealth of prose, poetry, and scientific exposition landing in my lap has seemed a bit like manna from heaven, given my bibliophilic predisposition. I've done my best to squelch feelings of self‐conscious guilt (this is too good to be true) and, instead, have worked assiduously to catalogue at least 750 books, secure approximately 125 reviewers, and publish about 100 book reviews to date.Within the last few years, however, I have received a number of biographies of various stripes. Most have been written about luminaries in the field of conservation. In fact, most of the books are about Americans, by Americans, published by American publishing houses. And while I knew who these people were and, in general, what their life works were about, I knew little else.Enter Curt Meine, internationally renowned conservationist and author of an important book on the life of Aldo Leopold ( 1988. Aldo Leopold: his life and work, University of Wisconsin Press, Madison. ). Last year's rumor about all these great biographies that circulated among the journal's editorial staff soon transformed into an exciting commitment for something new. Dr. Meine agreed to prepare an "occasional contribution" to the book review section that highlights the wellspring of new biographies. The choice of books and the manner of the review is solely the work of Dr. Meine. His uncanny insights into the people about whom the books are written, as well as the authors of the books, render this contribution significant beyond information about the individual biographies. It is, in fact, a profoundly thoughtful piece, worthy of reading at least half a dozen times. Therefore, it is my great pleasure to introduce the first "occasional contribution" to the journal, one that serves as a remarkable tribute to those who have gone before and as a hallmark of the society's membership.Peggy L. Fiedler Book Review Editor
Mere presence of distractors: Another determining factor for the attentional blink1
Authors: Kawahara Jun‐Ichiro 
Published: July 2003

Abstract: When two visual targets are presented in rapid succession, perception of the second target is deteriorated if the temporal lag between the two targets is short (0–300 ms). This ‘attentional blink’ (AB) phenomenon has been believed to occur only when the second target is followed by a backward mask or when there is a task switching between two targets. The present study revealed another determining factor for the occurrence of the AB, the presence or absence of a distractor stream. Five experiments examined the effect of possible confounding factors in the extant literature and suggested that the mere presence of a distractor stream affects the processing of targets even when the observers tried to ignore them, resulting in a processing delay. This effect is discussed in a model of AB deficit in terms of decay of the second target's representation.
The effects of lesions in the central nucleus of the amygdala on appetitive classical conditioning in rats
Authors: Tazumi Tooru , Okaichi Hiroshige 
Published: July 2003

Abstract:Lesions in the central nucleus of the amygdala (cAMY) have been known to interfere with the acquisition of fear classical conditioning when footshock is used as an unconditioned stimulus (US). The present study examined whether or not a similar interference would occur with an appetitive US. Five rats with lesions in the cAMY (the cAMY group), and eight unoperated control rats were trained in an appetitive classical conditioning paradigm, which did not include elements of operant learning, using a visual conditioned stimulus (CS) (5 W of light for 10 s duration) paired with a food pellet US (45 mg, cheese flavor). The behavioral index of appetitive conditioning was an increase in rearing approach behavior to the CS after CS and US pairings. During CS and US pairings, the movement of the rat was limited so that this approach behavior could not occur. As a result, all control rats showed an increase in rearing, but the cAMY group did not. These results suggest that the cAMY is critical for appetitive as well as fear classical conditioning.