bluuebunny/crossref_metadata_2025 huggingface dataset:
A strand‐specific model for chromosome segregation in bacteria
Authors: Rocha Eduardo P. C. , Fralick Joe , Vediyappan Govindsamy , Danchin Antoine , Norris Vic
Published: July 2003

Chromosome separation and segregation must be executed within a bacterial cell in which the membrane and cytoplasm are highly structured. Here, we develop a strand‐specific model based on each of the future daughter chromosomes being associated with a different set of structures or hyperstructures in an asymmetric cell. The essence of the segregation mechanism is that the genes on the same strand in the parental cell that are expressed together in a hyperstructure continue to be expressed together and segregate together in the daughter cell. The model therefore requires an asymmetric distribution of classes of genes and of binding sites and other structures on the strands of the parental chromosome. We show that the model is consistent with the asymmetric distribution of highly expressed genes and of stress response genes in Escherichia coli and Bacillus subtilis. The model offers a framework for interpreting data from genomics.
Prion protein gene polymorphisms in Saccharomyces cerevisiae
Authors: Resende Catarina G. , Outeiro Tiago F. , Sands Laina , Lindquist Susan , Tuite Mick F.
Published: July 2003

The yeast Saccharomyces cerevisiae genome encodes several proteins that, in laboratory strains, can take up a stable, transmissible prion form. In each case, this requires the Asn/Gln‐rich prion‐forming domain (PrD) of the protein to be intact. In order to further understand the evolutionary significance of this unusual property, we have examined four different prion genes and their corresponding PrDs, from a number of naturally occurring strains of S. cerevisiae. In 4 of the 16 strains studied we identified a new allele of the SUP35 gene (SUP35Δ19) that contains a 19‐amino‐acid deletion within the N‐terminal PrD, a deletion that eliminates the prion property of Sup35p. In these strains a second prion gene, RNQ1, was found to be highly polymorphic, with eight different RNQ1 alleles detected in the six diploid strains studied. In contrast, for one other prion gene (URE2) and the sequence of the NEW1 gene encoding a PrD, no significant degree of DNA polymorphism was detected. Analysis of the naturally occurring alleles of RNQ1 and SUP35 indicated that the various polymorphisms identified were associated with DNA tandem repeats (6, 12, 33, 42 or 57 bp) within the coding sequences. The expansion and contraction of DNA repeats within the RNQ1 gene may provide an evolutionary mechanism that can ensure rapid change between the [PRION+] and [prion–] states.
Co‐operative interactions control conjugative transfer of broad host‐range plasmid RK2: full effect of minor changes in TrbA operator depends on KorB
Authors: Bingle Lewis E.H. , Zatyka Malgorzata , Manzoor Susan E. , Thomas Christopher M.
Published: July 2003

A network of circuits, with KorB and TrbA as key regulators, controls genes for conjugative transfer of broad host range plasmid RK2. To assess the importance of the TrbA regulon, mutational analysis was applied to the TrbA operator at the trbB promoter and then to other TrbA‐regulated promoters in the tra region. All identified TrbA operators are submaximal; in the case of trbBp, a G to A transition that made the operator core a perfect palindrome increased repression by about 50% compared to the wild type. When this change was introduced into the RK2 genome, decreases in transfer frequency of up to three orders of magnitude were observed, with bigger effects when Escherichia coli was the donor compared to Pseudomonas putida. Western blotting showed a significant decrease in Trb protein levels. These effects were much greater than the effect of the mutation on repression by TrbA alone. When KorB was introduced into the reporter system, the effects were closer to those observed in the whole RK2 context. These results indicate that co‐operativity, previously observed between TrbA and KorB, allows big changes in transfer gene expression to result from small changes in individual regulator activities.
Tree root and soil heterotrophic respiration as revealed by girdling of boreal Scots pine forest: extending observations beyond the first year
Authors:   BHUPINDERPAL‐SINGH, NORDGREN A. , OTTOSSON LÖFVENIUS M. , HÖGBERG M. N. , MELLANDER P. ‐E. , HÖGBERG P.
Published: July 2003

Limitations in available techniques to separate autotrophic (root) and soil heterotrophic respiration have hampered the understanding of forest C cycling. The former is here defined as respiration by roots, their associated mycorrhizal fungi and other micro‐organisms in the rhizosphere directly dependent on labile C compounds leaked from roots. In order to separate the autotrophic and heterotrophic components of soil respiration, all Scots pine trees in 900 m2 plots were girdled to instantaneously terminate the supply of current photosynthates from the tree canopy to roots. Högberg et al. (Nature 411, 789–792, 2001) reported that autotrophic activity contributed up to 56% of total soil respiration during the first summer of this experiment. They also found that mobilization of stored starch (and likely also sugars) in roots after girdling caused an increased apparent heterotrophic respiration on girdled plots. Herein a transient increase in the δ13C of soil CO2 efflux after girdling, thought to be due to decomposition of 13C‐enriched ectomycorrhizal mycelium and root starch and sugar reserves, is reported. In the second year after girdling, when starch reserves of girdled tree roots were exhausted, calculated root respiration increased up to 65% of total soil CO2 efflux. It is suggested that this estimate of its contribution to soil respiration is more precise than the previous based on one year of observation. Heterotrophic respiration declined in response to a 20‐day‐long 6 °C decline in soil temperature during the second summer, whereas root respiration did not decline. This did not support the idea that root respiration should be more sensitive to variations in soil temperature. It is suggested that above‐ground photosynthetic activity and allocation patterns of recent photosynthates to roots should be considered in models of responses of forest C balances to global climate change.
Leaf, floret and seed infection of wheat by Pyrenophora semeniperda
Authors: Campbell M. A. , Medd R. W.
Published: July 2003

Infection processes of Pyrenophora semeniperda on seedling and adult wheat leaves and wheat ears were investigated. Almost 100% germination of conidia occurred on seedling leaves, compared with 20–30% on adult leaves. Appressoria formed over the anticlinal epidermal cell walls and haloes always accompanied infection. Sometimes papillae formed within the leaves as a resistance mechanism. Infection hyphae ramified through the intercellular spaces of the mesophyll resulting in cellular disruption. The infection processes on floral tissues were similar to those observed on leaves; however, no infection occurred on anther, stigmatic or stylar tissues. Infection of ovarian tissue occurred both with and without appressoria formation. Hyphae grew mainly in the epidermal layers and appeared unable to breach the integumental layer as no growth was observed in endosperm or embryo tissues. The optimum dew period temperature for conidial germination was 23·6°C, compared with 19·9°C for lesion development, 20·4°C for the production of infection structures on seedling leaves and 23·7°C for floret infection. Leaf disease development occurred in a logistic manner in response to dew period, with maximum infection observed after 21 h compared with > 48 h in seeds. An initial dark phase during the dew period was necessary for infection and temperature after the dew period had an effect, with significantly more numerous and larger lesions being formed at 15°C compared with 30°C. Seedling leaves were found to be more susceptible than older leaves, under both field and controlled environment conditions. Infection of wheat seeds following inoculation of ears, or after harvest burial of inoculated disease‐free seeds, was demonstrated. In the latter, 3‐week‐old seedlings were slightly stunted, whereas older plants were unaffected. The apparent unimportance of this plant pathogen as a cause of leaf disease in relation to its poor adaptation to dew periods and dew period temperature is discussed, along with the importance of its seed borne characteristics.
An optimized screening method for identifying levels of resistance to Crinipellis perniciosa in cocoa (Theobroma cacao)
Authors: Surujdeo‐Maharaj S. , Umaharan P. , Butler D. R. , Sreenivasan T. N.
Published: July 2003

The effects of host age, leaf number, host type (clone or seedling), pathogen spore concentration and incubation time on inoculation with Crinipellis perniciosa (witches’ broom disease of cocoa) were studied in greenhouse experiments using susceptible cocoa genotypes. Three methods of inoculation (agar‐drop, water‐drop and spray) were also tested. An optimized inoculation method was selected and tested for its repeatability as well as its ability to discriminate between various levels of resistance to C. perniciosa in cocoa. The optimized method (350 000 viable basidiospores per mL, 60 h incubation, agar‐drop technique) produced 100% infection repeatedly, on both clonal and seedling plants of a susceptible genotype. Seedling age (2–12 months) and leaf number did not significantly affect the percentage of plants with symptoms or broom characteristics. This method discriminated effectively between the various levels of resistance in 14 cocoa genotypes and is recommended as an inoculation method to identify levels of resistance in germplasm collections. Symptom severity was shown to be a better measure of resistance than infection success.
Phylogeny of the frosty pod rot pathogen of cocoa
Authors: Evans H. C. , Holmes K. A. , Reid A. P.
Published: July 2003

Morphological, cytological and molecular evidence is presented which confirms that the frosty pod rot pathogen of cocoa, formerly classified as the mitosporic fungusMoniliophthora roreri(Deuteromycota), belongs to the hymenomycetous genusCrinipellis(Basidiomycota) and that two varieties should now be recognized:Crinipellis rorerivar.roreriand the new varietyC. rorerivar.gileri. The latter was collected onTheobroma gileri, an endemic tree of submontane forests in north‐west Ecuador, and can be distinguished from Ecuadorian and Peruvian isolates from cocoa (T. cacao) on the basis of spore morphology, incompatibility and nucleotide sequence data. As with var.roreri, meiosis is shown to occur within the dispersive and infective spore stage of var.gileriand these meiospores are interpreted to represent a much modified probasidium. In addition, in a field inoculation experiment, an isolate fromT. gileriproved to be noninfective to cocoa pods when compared with positive control strains isolated fromT. cacaoin western Ecuador andT. bicolorin eastern Ecuador. It is concluded that var.gileriis the vestigial progenitor of the frosty pod rot pathogen of cocoa, with a host range and distribution restricted toT. gileriin the mesic forests of north‐west South America.
Menadione sodium bisulphite: a novel plant defence activator which enhances local and systemic resistance to infection byLeptosphaeria maculansin oilseed rape
Authors: Borges A. A. , Cools H. J. , Lucas J. A.
Published: July 2003

Pretreatment of the first true leaves of oilseed rape plants (Brassica napuscv. Bristol) with menadione sodium bisulphite (MSB) locally and systemically induced resistance, as shown by reduced lesion size and number, to infection by the fungal pathogenLeptosphaeria maculans, the causal agent of stem canker. Using a known systemic activator of salicylic acid‐dependentPR‐1induction, acibenzolar‐S‐methyl (BTH;S‐methylbenzo[1,2,3]thiadiazole‐7‐carbothiate) as a comparison, real‐time PCR expression analysis of genes encoding a pathogenesis‐related protein 1 (PR‐1) and an ascorbate peroxidase (APX) demonstrated a systemic enhancement ofAPXexpression in MSB‐pretreated plants, with no effect onPR‐1expression, suggesting augmented reactive oxygen species production in MSB‐pretreated plants. The results demonstrate MSB to be an effective resistance activator in oilseed rape, and potentially useful for the control of stem canker.
Breaching in fine sands and the generation of sustained turbidity currents in submarine canyons
Authors: Mastbergen Dick R. , Van Den Berg Jan H.
Published: July 2003

Abstract Natural, moderately loosely packed sands can only erode from the surface of the bed after an increase in pore volume. Because of this shear dilatancy, negative pore pressures are generated in the bed. In cases of low permeability, these negative pressures are released relatively slowly, which retards the maximum rate of erosion. This effect is incorporated in a new, analytically derived, pick‐up function that can explain the observation of gradual retrogressive failure of very steep subaqueous slopes, sometimes more than 5 m high, in fine non‐cohesive sands. This process, termed ‘breaching’ in the field of sediment dredging, may produce large failures in sand bars or river banks. The analytical function that describes the breaching process in fine sand is incorporated in a one‐dimensional, steady‐state numerical model of turbidity currents describing the spatial development of flow. This model is applied to simulate a large ‘flushing’ event in Scripps Submarine Canyon, Pacific coast of California. Breach retrogradation and the successive evolution in time of the resulting turbidity current in the canyon are predicted in a sequence of discrete steps. Predicted velocities are compared with values measured during a flushing event. Implications for the interpretation of deep‐water massive sands are discussed.
Tectonic controls on spatio‐temporal development of depositional systems and generation of fining‐upward basin fills in a strike‐slip setting: Kyokpori Formation (Cretaceous), south‐west Korea
Authors: Kim S. B. , Chough S. K. , Chun S. S.
Published: July 2003

Abstract The Kyokpori Formation (Cretaceous), south‐west Korea, represents a small‐scale lacustrine strike‐slip basin and consists of an ≈ 290 m thick siliciclastic succession with abundant volcaniclasts. The succession can be organized into eight facies associations representing distinctive depositional environments: (I) subaqueous talus; (II) delta plain; (III) steep‐gradient large‐scale delta slope; (IV) base of delta slope to prodelta; (V) small‐scale nested Gilbert‐type delta; (VI) small‐scale delta‐lobe system; (VII) subaqueous fan; and (VIII) basin plain. Facies associations I, III and IV together constitute a large‐scale steep‐sloped delta system. Correlation of the sedimentary succession indicates that the formation comprises two depositional sequences: the lower coarsening‐ to fining‐upward succession (up to 215 m thick) and the upper fining‐upward succession (up to 75 m thick). Based on facies distribution, architecture and correlation of depositional sequences, three stages of basin evolution are reconstructed. Stage 1 is represented by thick coarse‐grained deposits in the lower succession that form subaqueous breccia talus and steep‐sloped gravelly delta systems along the northern and southern basin margins, respectively, and a sandy subaqueous fan system inside the basin, abutting against a basement high. This asymmetric facies distribution suggests a half‐graben structure for the basin, and the thick accumulation of coarse‐grained deposits most likely reflects rapid subsidence of the basin floor during the transtensional opening of the basin. Stage 2 is marked by sandy black shale deposits in the upper part of the lower succession. The black shale is readily correlated across the basin margins, indicating a basinwide transgression probably resulting from large‐scale dip slip suppressing the lateral slip component on basin‐bounding faults. Stage 3 is characterized by gravelly delta‐lobe deposits in the upper succession that are smaller in dimension and located more basinward than the deposits of marginal systems of the lower succession. This lakeward shift of depocentre suggests a loss of accommodation in the basin margins and quiescence of fault movements. This basin evolution model suggests that the rate of dip‐slip displacement on basin‐margin faults can be regarded as the prime control for determining stacking patterns of such basin fills. The resultant basinwide fining‐upward sequences deviate from the coarsening‐upward cycles of other transtensional basins and reveal the variety of stratigraphic architecture in strike‐slip basins controlled by the changes in relative sense and magnitude of fault movements at the basin margins.
Geomorphological and sequence stratigraphic variability in wave‐dominated, shoreface‐shelf parasequences
Authors: Hampson Gary J. , Storms Joep E. A.
Published: July 2003

Abstract Physical stratigraphy within shoreface‐shelf parasequences contains a detailed, but virtually unstudied, record of shallow‐marine processes over a range of historical and geological timescales. Using high‐quality outcrop data sets, it is possible to reconstruct ancient shoreface‐shelf morphology from clinoform surfaces, and to track the evolving morphology of the ancient shoreface‐shelf. Our results suggest that shoreface‐shelf morphology varied considerably in response to processes that operate over a range of timescales. (1) Individual clinoform surfaces form as a result of enhanced wave scour and/or sediment starvation, which may be driven by minor fluctuations in relative sea level, sediment supply and/or wave climate over short timescales (101−103 years). These external controls cannot be distinguished in vertical facies successions, but may potentially be differentiated by the resulting clinoform geometries. (2) Clinoform geometry and distribution changes systematically within a single parasequence, reflecting the cycle in sea level and/or sediment supply that produced the parasequence (102−105 years). These changes record steepening of the shoreface‐shelf profile during early progradation and maintenance of a relatively uniform profile during late progradation. Modern shorefaces are not representative of this stratigraphic variability. (3) Clinoform geometries vary greatly between different parasequences as a result of variations in parasequence stacking pattern and relict shelf morphology during shoreface progradation (105−108 years). These controls determine the external dimensions of the parasequence.
Petrography and chemistry of sandstones from the Swiss Molasse Basin: an archive of the Oligocene to Miocene evolution of the Central Alps
Authors: Von Eynatten Hilmar
Published: July 2003

Abstract Oligocene to Miocene fluvial sandstones from the Swiss Molasse Basin were analysed for sandstone framework composition, heavy minerals, whole‐rock geochemistry and detrital chrome spinel chemistry. Samples were taken from the proximal part of the basin close to the Alpine main thrust and are chronostratigraphically calibrated between 31 and 13 Ma. Sandstone composition allows the identification of different source rocks, and their variation in time and space place constraints on the Oligocene to Miocene evolution of the Central Alps. In the eastern part of the basin, sandstones document a normal unroofing sequence with the downcutting from Austroalpine sedimentary cover into Austroalpine crystalline rocks and, slightly later at ≈ 21 Ma, into Penninic ophiolites. In the central part, downcutting into crystalline basement rocks occurred at ≈ 25 Ma, and the removal of the sedimentary cover was much more advanced than in the east. This may be interpreted as a first signal from the doming of the Lepontine area. At ≈ 20 Ma, extensional tectonics in the hinterland led to the first exposure of low‐grade metamorphic rocks from the footwall of the Simplon Fault in the Central Alps. Erosion of these rocks persisted up to the youngest sediments at ≈ 13 Ma. In the western part of the basin, a contribution from granitoid and (ultra)mafic rocks is documented as early as ≈ 28 Ma. The source for the (ultra)mafic detritus is Penninic ophiolites from the Piemonte zone of the western Alps, which were already exposed at the surface at that time.
Pseudofaults resulting from compartmentalized Liesegang bands: update
Authors: McBride Earle F.
Published: July 2003

Abstract Liesegang bands with apparent offset along fractures are common in some calcisiltite beds. Thin sections show, however, that primary laminations are not offset along the fractures. Following the development of fracture sets in the calcisiltite, the fractures were cemented by calcite. This formed polyhedral compartments of low‐permeability calcisiltite bounded by impermeable walls of calcite. Liesegang bands formed when oxygen in ground water diffused into polyhedra containing soluble ferrous iron in pore water. Each joint‐bounded polyhedral compartment behaved as an independent diffusion cell. Liesegang bands with nearly the same pattern and thickness tended to develop in adjacent compartments, but not at the same stratigraphic level; this resulted in the formation of pseudofaults.
Radiaxial fibrous calcites as low‐magnesian calcite cement precipitated in a marine‐meteoric mixing zone
Authors: Kim Yongin , Lee Yong Il
Published: July 2003

Abstract Radiaxial fibrous calcite (RFC) has previously been interpreted as a marine or replacive cement. Study of the Dongjeom Formation (Early Ordovician), Korea, shows that RFC can form in marine‐meteoric mixing zones as a low‐magnesian calcite (LMC) cement. RFC in the shallow‐marine Dongjeom Formation occurs in arenaceous limestones at the top of a transgressive facies overlying a regressive facies. It shows well‐developed growth zonation, and lighter oxygen isotope values and more radiogenic strontium isotope ratios than those of Early Ordovician marine calcite. Such petrographic and chemical evidence indicates that the RFC was precipitated as a primary LMC cement in a marine and meteoric mixing zone. Owing to the unique environment of formation, the Dongjeom RFC is characterized by growth zonal fabric comprising alternating subzones, which may indicate precipitation from varying fluids. In addition, this study documents the importance of substrate for development of RFC. Early ‘nucleation’ for RFC occurred mainly on microcrystalline skeletal grains and internal sediments, whereas on homogeneously altered substrates, thin‐coated banding structure developed, ultimately forming coarse crystalline spar. This suggests that microcrystalline substrates are preferred sites for nucleation of RFC.
Sedimentary architecture and genesis of Holocene shallow‐water mud‐mounds, northern Belize
Authors: Mazzullo S. J. , Teal Chellie S. , Bischoff William D. , Dimmick‐Wells Kimberly , Wilhite Brian W.
Published: July 2003

Abstract Cangrejo and Bulkhead Shoals are areally extensive, Holocene biodetrital mud‐mounds in northern Belize. They encompass areas of 20 km2 and 35 km2 in distal and proximal positions, respectively, on a wide and shallow‐water, microtidal carbonate shelf where storms are the major process affecting sediment dynamics. Sediments at each mound are primarily biodetrital and comprise part of a eustatically forced, dominantly subtidal cycle with a recognizable deepening‐upward transgressive systems tract, condensed section and shallowing‐upward highstand systems tract. Antecedent topographic relief on Pleistocene limestone bedrock also provided marine accommodation space for deposition of sediments that are a maximum of 7·6 m thick at Cangrejo and 4·5 m thick at Bulkhead. Despite differences in energy levels and location, facies and internal sedimentological architectures of the mud‐mounds are similar. On top of Pleistocene limestone or buried soil developed on it are mangrove peat and overlying to laterally correlative shelly gravels. Deposition of these basal transgressive, premound facies tracked the rapid rate of sea‐level rise from about 6400–6500 years BP to 4500 years BP, and the thin basal sedimentation unit of the overlying mound‐core appears to be a condensed section. Following this, the thick and complex facies mosaic comprising mound‐cores represents highstand systems tract sediments deposited in the last

≈ 4500 years during slow and decelerating sea‐level rise. Within these sections, there is an early phase of progradationally offlapping catch‐up deposition and a later (and current) phase of aggradational keep‐up deposition. The mound‐cores comprise stacked storm‐deposited autogenic sedimentation units, the upper bounding surfaces of which are mostly eroded former sediment–water interfaces below which depositional textures have largely been overprinted by biogenic processes associated with Thalassia‐colonized surfaces. Vertical stacking of these units imparts a quasi‐cyclic architecture to the section that superficially mimics metre‐scale parasequences in ancient rocks. The locations of the mud‐mounds and the tidal channels transecting them have apparently been stable over the last 50 years. Characteristics that might distinguish these mud‐mounds and those mudbanks deposited in more restricted settings such as Florida Bay are their broad areal extent, high proportion of sand‐size sediment fractions and relatively abundant biotic particles derived from adjoining open shelf areas.
The effect of surface moisture on the entrainment of dune sand by wind: an evaluation of selected models
Authors: Cornelis W. M. , Gabriels D.
Published: July 2003

Abstract Reliable predictions of wind erosion depend on the accuracy of determining whether erosion occurs or not. Among the several factors that govern the initiation of soil movement by wind, surface moisture is one of the most significant. Some widely used models that predict the threshold shear velocity for particle detachment of wet soils by wind were critically reviewed and evaluated. Wind‐tunnel experiments were conducted on pre‐wetted dune sand with moisture contents ranging from 0·00 to 0·04 kg kg−1. Sand samples were exposed to different wind speeds for 2 min. Moisture content was determined gravimetrically before and after each experiment, and the saltation of sand particles was recorded electronically with a saltiphone. Shear velocities were deduced from the wind speed profiles. For each moisture content, the experiments were repeated at different shear velocities, with the threshold shear velocity being determined by least‐squares analysis of the relationships between particle number rates and shear velocity.

Within the 2‐min test runs, temporal changes in particle number rates and moisture contents were detected. A steep increase in the threshold shear velocity with moisture content was observed. When comparing the models, large differences between the predicted results became apparent. At a moisture content of 0·007 kg kg−1, which is half the moisture content retained to the soil matrix at a water tension (or matric potential) of −1·5 MPa, the increase in ‘wet’ threshold shear velocity predicted with the different models relative to the dry threshold shear velocity ranged from 117% to 171%. The highest care should therefore be taken when using current models to predict the threshold shear velocity of wet sediment. Nevertheless, the models of Chepil (1956; Proc. Soil Sci. Soc. Am., 20, 288–292) and Saleh & Fryrear (1995; Soil Sci., 160, 304–309) are the best alternatives available.
Loading fractures and Liesegang laminae: new sedimentary structures found in the north‐western North Alpine Foreland Basin (Oligocene–Miocene, south‐west Germany)
Authors: Tipper John C. , Sach Volker J. , Heizmann Elmar P. J.
Published: July 2003

Abstract Spectacular sedimentary structures recently found in the Molasse Basin (Oligocene–Miocene) in southern Germany were produced by soft‐sediment deformation under highly unusual conditions. These large, apparently wedge‐like structures –‘loading fractures’– cut down into beds of marl and are filled with coarse sand and intraclasts of shale. Wrapping the sides of the structures is a thin, continuous bed of layered dark claystone – the ‘DCB’. The upper and lower layers of this bed are an organic‐rich clay; the middle layer is a laminated quartzite. The precursor of the DCB was a lacustrine gyttja rich in diatom frustules. It was supersaturated in silica as it was buried. Subsequent diffusion of oxygen into this gyttja at a burial depth of only a few metres resulted in the formation of Liesegang laminae of quartz. These laminae grew and amalgamated, forming the layer of laminated quartzite. The sediments overlying the DCB were eventually removed by erosion, probably in a high‐energy marine environment. This erosion cut down to the DCB but was unable to penetrate it. The DCB remained exposed on the sea floor until a sudden depositional event occurred – the deposition of a 2·5 metre thick bed of coarse sand with shale intraclasts. Although the DCB had been able to resist the submarine erosion, it could not support the load of this new bed. The quartzite layer in it therefore fractured, transferring that load down onto the underlying, still‐unconsolidated marl. The intraclast‐rich sands were forced down into this marl, carrying ahead of them the partly broken remains of the DCB.
Mesozoic high‐Ba–Sr granitoids from North China: geochemical characteristics and geological implications
Authors: Qian Qing , Chung Sun‐Lin , Lee Tung‐Yi , Wen Da‐Jen
Published: July 2003

Abstract Mesozoic magmatism occurred extensively in the North China block (NCB) and the Dabie–Sulu orogen (DSO) post‐dating the North–South China collision, resulting in abundant intrusive and volcanic rocks ranging from basic to acidic compositions. The intermediate‐acidic intrusive rocks can be grouped into two types, namely high‐Ba–Sr granitoids and low‐Ba–Sr granitoids that both have distinct geochemical characteristics. The high‐Ba–Sr granitoids are similar in most of the incompatible trace element systematics to the associated basic rocks, which probably originated from melting of subcontinental lithospheric mantle, indicating significant mantle contributions to them. Geochemical similarities are observed between the basic rocks from the NCB and DSO, implying a regional‐scale magma‐generating mechanism and that mantle enrichment beneath the DSO was independent from the Triassic deep continental subduction in the region. We therefore interpret that the Mesozoic magmatism resulted from delamination of the ancient lithospheric mantle beneath the eastern part of North China.
Calcarenite and sapropel deposition in the Mediterranean Pliocene: shallow‐ and deep‐water record of astronomically driven climatic events
Authors: Roveri Marco , Taviani Marco
Published: July 2003

ABSTRACT Calcarenitic bodies punctuate the shallow‐water deposits of Plio‐Pleistocene Mediterranean basins. Their rhythmic stacking pattern and stratigraphic distribution suggest a close relationship with deep‐water sapropel cycles, whose development is controlled by periodic changes in the Earth's orbital parameters. Calcarenitic bodies occur as eccentricity‐controlled clusters (over periods of 100–400 kyr) showing a time‐correlation with sapropel clusters, starting from 3.1 Ma. Formation of individual calcarenites is possibly driven by obliquity and/or precession cyclicity. This has important implications both for an improved understanding of Mediterranean palaeoceanographic events and correlation of shallow‐ and deep‐water successions. The appearance of sapropel and calcarenitic clusters starting from 3.1 Ma suggests a direct link with the onset of Northern Hemisphere glaciation, which could be responsible for the amplification of oceanographic events within the Mediterranean.
A method for profiling classes of plant hormones and their metabolites using liquid chromatography‐electrospray ionization tandem mass spectrometry: an analysis of hormone regulation of thermodormancy of lettuce (Lactuca sativa L.) seeds
Authors: Chiwocha Sheila D. S. , Abrams Suzanne R. , Ambrose Stephen J. , Cutler Adrian J. , Loewen Mary , Ross Andrew R. S. , Kermode Allison R.
Published: July 2003

A highly selective and sensitive method for the simultaneous analysis of several plant hormones and their metabolites is described. The method combines high‐performance liquid chromatography (HPLC) with positive and negative electrospray ionization‐tandem mass spectrometry (ESI–MS/MS) to quantify a broad range of chemically and structurally diverse compounds. The addition of deuterium‐labeled analogs for these compounds prior to sample extraction permits accurate quantification by multiple reaction monitoring (MRM). Endogenous levels of abscisic acid (ABA), abscisic acid glucose ester (ABA‐GE), 7′‐hydroxy‐abscisic acid (7′‐OH‐ABA), phaseic acid (PA), dihydrophaseic acid (DPA), indole‐3‐acetic acid (IAA), indole‐3‐aspartate (IAAsp), zeatin (Z), zeatin riboside (ZR), isopentenyladenine (2iP), isopentenyladenosine (IPA), and gibberellins (GA)1, GA3, GA4, and GA7 were determined simultaneously in a single run. Detection limits ranged from 0.682 fmol for Z to 1.53 pmol for ABA. The method was applied to the analysis of plant hormones and hormonal metabolites associated with seed dormancy and germination in lettuce (Lactuca sativa L. cv. Grand Rapids), using extracts from only 50 to 100 mg DW of seed. Thermodormancy was induced by incubating seeds at 33°C instead of 23°C. Germinating seeds transiently accumulated high levels of ABA‐GE. In contrast, thermodormant seeds transiently accumulated high levels of DPA after 7 days at 33°C. GA1 and GA3 were detected during germination, and levels of GA1 increased during early post‐germinative growth. After several days of incubation, thermodormant seeds exhibited a striking transient accumulation of IAA, which did not occur in seeds germinating at 23°C. We conclude that hormone metabolism in thermodormant seeds is surprisingly active and is significantly different from that of germinating seeds.
Acceleration of Aux/IAA proteolysis is specific for auxin and independent of AXR1
Authors: Zenser Nathan , Dreher Kate A. , Edwards Stephanie R. , Callis Judy
Published: July 2003

Aux/IAA proteins are short‐lived transcriptional regulators involved in auxin signaling. Using Aux/IAA luciferase (LUC) fusion proteins expressed in Arabidopsis thaliana, we previously showed that rapid degradation of these proteins requires conserved Aux/IAA domain II and that exogenous auxin accelerates their degradation. To further examine auxin‐mediated increases in proteolysis, the degradation of two other LUC fusion proteins, a non‐cleavable ubiquitin LUC fusion (UB1–72::LUC) and SAUR15::LUC was determined in vivo in seedlings. Their half‐lives were 20 ± 4 and 104 ± 10 min, respectively. SAUR15::LUC half‐life was not affected by pre‐incubation with 2,4‐D. Auxin did not have an equivalent effect on UB(1–72)::LUC steady‐state levels as compared to PsIAA6:LUC. LUC fused to an Aux/IAA domain II degraded more rapidly following auxin application, demonstrating that this region is sufficient for auxin‐mediated acceleration of proteolysis. Hormonal cross‐talk at the level of Aux/IAA proteolysis was examined. 1‐aminocyclopropane‐1‐carboxylic acid (ACC), benzyladenine (BA), abscisic acid (ABA), and brassinolide (BL) did not affect the degradation rate of IAA1::LUC, and gibberellic acid (GA3) and salicylic acid (SA) did not specifically affect the steady‐state levels of Aux/IAA::LUC proteins. An Aux/IAA::LUC transgene was crossed into the auxin resistant‐1 (axr1–12) background. In axr1–12, the half‐life of PsIAA6(1–73)::LUC increased 4.5‐fold, but proteolysis still accelerated in response to exogenous auxin. These data suggest that auxin is the only phytohormone that accelerates Aux/IAA proteolysis, and that this acceleration is specific for Aux/IAA proteins. In addition, AXR1 plays an important role in rapid basal proteolysis of Aux/IAA proteins, but is not required for auxin‐mediated acceleration of their degradation.
The soybean NRAMP homologue, GmDMT1, is a symbiotic divalent metal transporter capable of ferrous iron transport
Authors: Kaiser Brent N. , Moreau Sophie , Castelli Joanne , Thomson Rowena , Lambert Annie , Bogliolo Stéphanie , Puppo Alain , Day David A.
Published: July 2003

Iron is an important nutrient in N2‐fixing legume root nodules. Iron supplied to the nodule is used by the plant for the synthesis of leghemoglobin, while in the bacteroid fraction, it is used as an essential cofactor for the bacterial N2‐fixing enzyme, nitrogenase, and iron‐containing proteins of the electron transport chain. The supply of iron to the bacteroids requires initial transport across the plant‐derived peribacteroid membrane, which physically separates bacteroids from the infected plant cell cytosol. In this study, we have identified Glycine max divalent metal transporter 1 (GmDmt1), a soybean homologue of the NRAMP/Dmt1 family of divalent metal ion transporters. GmDmt1 shows enhanced expression in soybean root nodules and is most highly expressed at the onset of nitrogen fixation in developing nodules. Antibodies raised against a partial fragment of GmDmt1 confirmed its presence on the peribacteroid membrane (PBM) of soybean root nodules. GmDmt1 was able to both rescue growth and enhance 55Fe(II) uptake in the ferrous iron transport deficient yeast strain (fet3fet4). The results indicate that GmDmt1 is a nodule‐enhanced transporter capable of ferrous iron transport across the PBM of soybean root nodules. Its role in nodule iron homeostasis to support bacterial nitrogen fixation is discussed.
Rapid migration in gel filtration of the Cf‐4 and Cf‐9 resistance proteins is an intrinsic property of Cf proteins and not because of their association with high‐molecular‐weight proteins
Authors: Van der Hoorn Renier A. L. , Rivas Susana , Wulff Brande B. H. , Jones Jonathan D. G. , Joosten Matthieu H. A. J.
Published: July 2003

Gel filtration is frequently used to study the behaviour and composition of protein complexes. In previous studies, gel filtration analysis of solubilised membranes containing the tomato Cf‐4 and Cf‐9 resistance proteins indicated that these Cf proteins are present in an approximately 400‐ and 420‐kDa protein complex, respectively, which contains only one Cf molecule per complex, does not contain Rho‐related proteins, and does not alter in size upon elicitation. Here, we show that inactive Cf‐4 and Cf‐9 mutant proteins have a similar large apparent size upon gel filtration analysis. The size remains unaltered after pre‐treating the samples under harsh conditions, such as boiling with SDS and incubation in 6 m urea. A similar large apparent size was found for Cf‐4 and Cf‐9 isolated from SDS gel and for Cf‐9 expressed by insect cells. Therefore, the large apparent size observed in our studies appears to be an intrinsic property of the Cf proteins, rather than being caused by association with high‐molecular‐weight protein(s). Taken together, these results suggest that caution should be taken when interpreting data obtained from gel filtration of LRR‐containing proteins.
The Arabidopsis mutant dct is deficient in the plastidic glutamate/malate translocator DiT2
Authors: Renné Petra , Dreßen Uta , Hebbeker Ulrike , Hille Diana , Flügge Ulf‐Ingo , Westhoff Peter , Weber Andreas P. M.
Published: July 2003

The Arabidopsis mutant dicarboxylate transport (dct) is one of the classic mutants in the photorespiratory pathway. It requires high CO2 levels for survival. Physiologic and biochemical characterization of dct indicated that dct is deficient in the transport of dicarboxylates across the chloroplast envelope membrane. Hence, re‐assimilation of ammonia generated by the photorespiratory cycle is blocked. However, the defective gene in dct has not been identified at the molecular level. Here, we report on the molecular characterization of the defective gene in dct, on the complementation of the mutant phenotype with a wild‐type cDNA, and on the functional characterization of the gene product, DiT2, in a recombinant reconstituted system. Furthermore, we provide the kinetic constants of recombinant DiT1 and DiT2, and we discuss these data with respect to their functions in ammonia assimilation. Moreover, an analysis of the transcript levels of DiT1 and DiT2 in different C3‐ and C4‐type plant species is presented, and we demonstrate that the substrate specificity of DiT2 from the C4‐plant Flaveria bidentis is similar to its counterpart from C3 plants.
Classification and identification of Arabidopsis cell wall mutants using Fourier‐Transform InfraRed (FT‐IR) microspectroscopy
Authors: Mouille Grégory , Robin Stéphane , Lecomte Mannaïg , Pagant Silvère , Höfte Herman
Published: July 2003

We have developed a novel procedure for the rapid classification and identification of Arabidopsis mutants with altered cell wall architecture based on Fourier‐Transform Infrared (FT‐IR) microspectroscopy. FT‐IR transmission spectra were sampled from native 4‐day‐old dark‐grown hypocotyls of 46 mutants and the wild type treated with various drugs. The Mahalanobis distance between mutants, calculated from the spectral information after compression with the Discriminant Variables Selection procedure, was used for α hierarchical cluster analysis. Despite the completely unsupervised nature of the classification procedure, we show that all mutants with cellulose defects appeared in the same cluster. In addition, mutant alleles of similar strength for several unrelated loci were also clustered, which demonstrates the sensitivity of the method to detect a wide array of cell wall defects. Comparing the cellulose‐deficient cluster with the cluster that contained wild‐type controls led to the identification of wave numbers that were diagnostic for altered cellulose content in the context of an intact cell wall. The results show that FT‐IR spectra can be used to identify different classes of mutants and to characterize cell wall changes at a microscopic level in unknown mutants. This procedure significantly accelerates the identification and classification of cell wall mutants, which makes cell wall polysaccharides more accessible to functional genomics approaches.
Development of enhancer trap lines for functional analysis of the rice genome
Authors: Wu Changyin , Li Xiangjun , Yuan Wenya , Chen Guoxing , Kilian Andrzej , Li Juan , Xu Caiguo , Li Xianghua , Zhou Dao‐Xiu , Wang Shiping , Zhang Qifa
Published: July 2003

Enhancer trapping has provided a powerful strategy for identifying novel genes and regulatory elements. In this study, we adopted an enhancer trap system, consisting of the GAL4/VP16–UAS elements with GUS as the reporter, to generate a trapping population of rice. Currently, 31 443 independent transformants were obtained from two cultivars using Agrobacterium‐mediated T‐DNA insertion. PCR tests and DNA blot hybridization showed that about 94% of the transformants contained T‐DNA insertions. The transformants carried, on average, two copies of the T‐DNA, and 42% of the transformants had single‐copy insertions. Histochemical assays of approximately 1000 T0 plants revealed various patterns of the reporter gene expression, including expression in only one tissue, and simultaneously in two or more tissues. The expression pattern of the reporter gene in T1 families corresponded well with the T0 plants and segregated in a 3 : 1 Mendelian ratio in majority of the T1 families tested. The frequency of reporter gene expression in the enhancer trap lines was much higher than that in gene trap lines reported previously. Analysis of flanking sequences of T‐DNA insertion sites from about 200 transformants showed that almost all the sequences had homology with the sequences in the rice genome databases. Morphologically conspicuous mutations were observed in about 7.5% of the 2679 T1 families that were field‐tested, and segregation in more than one‐third of the families fit the 3 : 1 ratio. It was concluded that GAL4/VP16–UAS elements provided a useful system for enhancer trap in rice.
Transgenic tobacco plants expressing antisense ferredoxin‐NADP(H) reductase transcripts display increased susceptibility to photo‐oxidative damage
Authors: Palatnik Javier F. , Tognetti Vanesa B. , Poli Hugo O. , Rodríguez Ramiro E. , Blanco Nicolás , Gattuso Martha , Hajirezaei Mohammad‐Reza , Sonnewald Uwe , Valle Estela M. , Carrillo Néstor
Published: July 2003

Ferredoxin‐NADP(H) reductase (FNR) catalyses the final step of the photosynthetic electron transport in chloroplasts. Using an antisense RNA strategy to reduce expression of this flavoenzyme in transgenic tobacco plants, it has been demonstrated that FNR mediates a rate‐limiting step of photosynthesis under both limiting and saturating light conditions. Here, we show that these FNR‐deficient plants are abnormally prone to photo‐oxidative injury. When grown under autotrophic conditions for 3 weeks, specimens with 20–40% extant reductase undergo leaf bleaching, lipid peroxidation and membrane damage. The magnitude of the effect was proportional to the light intensity and to the extent of FNR depletion, and was accompanied by morphological changes involving accumulation of aberrant plastids with defective thylakoid stacking. Damage was initially confined to chloroplast membranes, whereas Rubisco and other stromal proteins began to decline only after several weeks of autotrophic growth, paralleled by partial recovery of NADPH levels. Exposure of the transgenic plants to moderately high irradiation resulted in rapid loss of photosynthetic capacity and accumulation of singlet oxygen in leaves. The collected results suggest that the extensive photo‐oxidative damage sustained by plants impaired in FNR expression was caused by singlet oxygen building up to toxic levels in these tissues, as a direct consequence of the over‐reduction of the electron transport chain in FNR‐deficient chloroplasts.
A gene encoding an RNase D exonuclease‐like protein is required for post‐transcriptional silencing in Arabidopsis
Authors: Glazov Eugene , Phillips Kenneth , Budziszewski Gregory J. , Meins Frederick , Levin Joshua Z.
Published: July 2003

Post‐transcriptional gene silencing (PTGS) and the closely related phenomenon RNA interference (RNAi) result from the initial endonucleolytic cleavage of target mRNAs, which are then presumed to be completely hydrolyzed by exoribonucleases. To date, no plant genes required for PTGS are known to encode exoribonucleases. The Arabidopsis Werner Syndrome‐like exonuclease (WEX) gene encodes an RNase D domain most similar to that in human Werner Syndrome protein (WRN), but lacks the RecQ helicase domain. It is also related to Caenorhabditis elegans mut‐7, which is essential for RNAi, PTGS, and transposon activity. We isolated a loss‐of‐function mutant, wex‐1, that showed greatly reduced expression of WEX mRNA and early flowering. Although wex‐1 did not affect expression of a robust marker for transcriptional gene silencing (TGS), PTGS of a green‐fluorescent‐protein (GFP) reporter gene was blocked in wex‐1 and restored by ectopic expression of WEX, indicating that WEX is required for PTGS but not TGS. Thus, members of the RNase D protein family are required for PTGS in both plants and animals. Interestingly, WEX has been shown to interact with an Arabidopsis RecQ helicase, suggesting that these proteins might comprise a functional equivalent of WRN.