bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial and temporal distribution of diagenetic alterations in siliciclastic rocks: implications for mass transfer in sedimentary basins
Authors: Morad S. , Ketzer J. M. , De Ros L. F.
Published: March 2003

The spatial and temporal distribution of diagenetic alterations in siliciclastic sequences is controlled by a complex array of interrelated parameters that prevail during eodiagenesis, mesodiagenesis and telodiagenesis. The spatial distribution of near‐surface eogenetic alteration is controlled by depositional facies, climate, detrital composition and relative changes in sea‐level. The most important eogenetic alterations in continental sediments include silicate dissolution and the formation of kaolinite, smectite, calcrete and dolocrete. In marine and transitional sediments, eogenetic alterations include the precipitation of carbonate, opal, microquartz, Fe‐silicates (glaucony, berthierine and nontronite), sulphides and zeolite. The eogenetic evolution of marine and transitional sediments can probably be developed within a predictable sequence stratigraphic context. Mesodiagenesis is strongly influenced by the induced eogenetic alterations, as well as by temperature, pressure and the composition of basinal brines. The residence time of sedimentary sequences under certain burial conditions is of key importance in determining the timing, extent and patterns of diagenetic modifications induced. The most important mesogenetic alterations include feldspar albitization, illitization and chloritization of smectite and kaolinite, dickitization of kaolinite, chemical compaction as well as quartz and carbonate cementation. Various aspects of deep‐burial mesodiagenesis are still poorly understood, such as: (i) whether reactions are accomplished by active fluid flow or by diffusion; (ii) the pattern and extent of mass transfer between mudrocks and sandstones; (iii) the role of hydrocarbon emplacement on sandstone diagenesis; and (iv) the importance and origin of fluids involved in the formation of secondary inter‐ and intragranular porosity during mesodiagenesis. Uplift and incursion of meteoric waters induce telogenetic alterations that include kaolinitization and carbonate‐cement dissolution down to depths of tens to a few hundred metres below the surface.
Punctuated environmental change along the Holocene (<6 ka) bank margin of south‐west Exuma Sound, Bahamas
Authors: Dix George R. , Kyser Kurt
Published: March 2003

Characteristics of environmental change along the Holocene (<6 ka BP) bank margin of south‐west Exuma Sound, Bahamas, are defined by comparing mineral, isotope and lithologic stratigraphic patterns in deep‐water (1081 m) slope strata in ODP Hole 631A (Exuma Sound) with proximal (≈6 km) shoal‐water and insular geology of the Lee Stocking Island (LSI) region. After platform submergence, a bank‐top transition from non‐skeletal‐ to skeletal‐dominated deposition occurred in the LSI region by ≈3·8 ka, and is recorded in the adjacent slope sediments by a contemporaneous change in the abundance of transported allochems. The transition at Site 631 is punctuated by an anomalous shift in foraminiferal δ13C (–1‰) and δ18O (–3‰), which may represent a period of climate change that established a brackish coastal zone at least 6 km wide, coincident (≈3·8–4 ka) with bank‐top erosion and pedogenesis. Non‐skeletal allochems reappeared in Hole 631A sediments as the dominant transported allochem type by ≈2·4 ka, then again over the last several hundred years, and are contemporaneous with periods of increased platform‐margin circulation in the LSI region. Such rejuvenation of platform circulation may have resulted from rapid relative rises in sea level, superimposed on the net gradual post‐glacial rise. At Site 631, a prominent (25%) decline in aragonite abundance occurred during the period from 2·4 ka to the last few hundred years, and coincided with an increase in magnesian calcite and skeletal debris, and a positive shift in foraminiferal δ18O values. These patterns lend support to the hypothesis that, during this period, the LSI margin was barred by skeletal shoals, allowing bank‐top trapping of aragonite and hypersaline water, with increased coastal salinity (resulting from reflux of hypersaline waters through the shoals) and/or cooled coastal waters (caused by reduced exchange of warmed bank‐derived water relative to wind‐generated upwelling). Along the Exuma slope, a diagenetic overprint may further enhance the recent decline in aragonite accumulation. Integration of Holocene deep‐water slope and bank‐top stratigraphies along the bank margin of south‐west Exuma Sound reveals a pattern of punctuated environmental change superimposed on longer term development of interglacial conditions.
Vertical and lateral organization of a carbonate deep‐water slope marginal to a submarine fan system, Miocene, southern Turkey
Authors: Cronin Bryan T. , GÜrbÜz Kemal , Hurst Andrew , Satur Nick
Published: March 2003

Organization is recognized in the forereef–deep water slope–submarine fan system of the Burdigalian‐Langhian Kaplankaya Formation. A basinwards transition from a prograding shelfal reef complex, through forereef talus, deep‐water slope and laterally encroaching bypass deep‐water clastic system is described, although the deep‐water slope makes up the bulk of the succession. Considerable thickness variations occur between the reef and deep‐water clastic complexes; these are controlled by sea‐floor topography, carbonate foreslope gradient and degree of mass wasting off the platform and foreslope. The vertical and lateral heterogeneity of the Kaplankaya deep‐water slope system is described from a number of localities along a 40‐km‐long and up to 3‐km‐wide exposed section of the northern margin of the Miocene Adana Basin, a foreland basin setting resulting from thrust sheet loading from the north during the Tauride Orogeny. Detailed field mapping is supplemented with vertical sedimentary logs, photomosaics, palaeontological and petrological data to investigate stratal variation, diagnostic architectural elements, controls on slope progradation, differential timing of basinward encroachment of the reefal complex and lateral onlap of the deep‐water clastic system onto the slope. Three‐dimensional models are presented showing the vertical and lateral facies associations in different parts of the deep‐water slope system, and provide a basis for architectural prediction of geometry and relative position in such environments.
Towards establishing criteria for identifying trigger mechanisms for soft‐sediment deformation: a case study of Late Pleistocene lacustrine sands and clays, Onikobe and Nakayamadaira Basins, northeastern Japan
Authors: Jones Alison P. , Omoto Kunio
Published: March 2003

Five main deformation units, discrete sheets of deformed sediments that lie between a significant thickness of undeformed sediment, were selected for study within Late Pleistocene lacustrine sands and clays in the Onikobe and Nakayamadaira Basins, northeastern Japan. The deformed units show evidence of deformation by a variety of mechanisms including fluidization, liquefaction, brittle failure and cohesive flow. Driving forces are thought to be primarily reverse density gradient systems, but also include gravitational body force, shear stress and unequal loading. The main trigger mechanisms are firstly earthquakes, secondly overloading from volcanic sands and thirdly, to a lesser extent, subaqueous currents. Consideration is given to criteria that allow the trigger mechanism to be identified. This study shows that the following criteria can be used to identify a seismic triggering agent: (i) setting; (ii) the extent of the deformation units; (iii) absence of evidence relating to other potential trigger mechanisms; and (iv) evidence relating to other potential trigger mechanisms is present but can be seen elsewhere in the stratigraphic section associated with undeformed sediment. Conversely, the following criteria, while they are important in interpreting the driving force and deformation mechanism, have no relevance to the trigger mechanism: (i) sediment composition; (ii) deformation structures being restricted to a single stratigraphic interval (<1 m thick) (not necessarily correlatable over large areas); and (iii) similarity to structures in the literature.
The structure and fluid mechanics of turbidity currents: a review of some recent studies and their geological implications
Authors: Kneller Ben , Buckee Clare
Published: March 2003

The literature on the structure and behaviour of gravity currents is reviewed, with emphasis on some recent studies, and with particular attention to turbidity currents, though reference is also made to comparable behaviour in pyroclastic flows. Questions of definition are discussed, in particular the distinction between dense currents, which may deposit en masse, and more dilute currents. High‐density dispersions may exist as a discrete, independently moving layer beneath a more dilute flow, as the basal part of a continuous density distribution or possibly as a transient depositional layer. Existing theory appears inadequate to explain the behaviour of some high‐density dispersions. Surge‐type currents are contrasted with quasi‐steady currents, which may be generated by a variety of mechanisms including direct feed by rivers in flood. Such fluvially generated currents provide one means of generating currents with reversing buoyancy. Geologically significant turbidity currents are impractical for direct study owing to their large scale and (often) destructive nature. Small‐scale laboratory currents offer a wealth of insights into turbidity current behaviour. This paper summarizes recent experimental studies that focus on the physical structure of gravity currents, with emphasis on the velocity and turbulence structure, the vertical density distribution and the stability of stratification. Preliminary quantification of the turbulence structure (including controls on turbulent entrainment, turbulent kinetic energy, Reynolds stresses and turbulence production) has been facilitated by recent technological developments that have allowed the measurement of instantaneous fluctuations in both velocity and concentration. Laboratory models, however, generally involve substantial simplification, and require compromises in some parameters to achieve adequate scaling of the parameters of most interest. Mathematical modelling also provides important insights into turbidity current behaviour. We discuss various approaches to modelling, ranging from simple hydraulic equations to systems of partial differential equations that explicitly treat conservation of momentum, fluid and sediment mass, and turbulent kinetic energy. The application for which the model is designed (i.e. to calculate mean head velocity or to create an instantaneous two‐dimensional contour plot of downstream velocity in a current) determines the complexity of the mathematical model required. The behaviour of suspension currents around topography is complex and depends upon the relative height of the topography, and upon the density and velocity structure of the current. Many interactions with topography are well described by the internal Froude number, Fri. Both reflection and deflection of currents may occur on the upstream side of topography, depending upon Fri. On the downstream side of topography, flow separation, lee waves or hydraulic jumps may occur.
Organic matter, putative nannobacteria and the formation of ooids and hardgrounds
Authors: Folk Robert L. , Leo Lynch F.
Published: March 2003

Modern ooids from Joulters Cay, when baked at 500 °C, turn various shades of black depending upon the organic content. Mucus‐rich laminae occur at quasi‐regular intervals of a few micrometres within the cortex. When mucus is still present, it turns black; when it is absent, there is a gap. The cortex consists of two types of aragonite: (1) ‘batons’ of circular cross‐section capped by a single 0·1‐μm (100‐nm) ball, which can be interpreted as a single nannobacteria cell that precipitated the baton; (2) elongate crystals made of multiple rows of minute balls of about 0·03 μm (30 nm), which may or may not have been small organisms in the size range of viruses. There are also some crystals that show no evidence of organic precipitation. Hardground cementation begins with the formation of a terminal mucus‐rich ring on the ooid that bakes black and is crowded with 0·1‐μm (100‐nm) balls. Some ooids are then joined by a meniscus also made of mucus with aragonite crystals. The final, most abundant hardground cement forms a fur of inorganic aragonite crystals often shaped like plywood sheets, although some ‘organic’, elongate crystals composed of ≈0·03 μm (≈30 nm) balls are also found in the later cement. For a century, ooids have been known to be closely associated with organic matter; this paper goes further and proposes that the bulk of the ooid may be precipitated by nannobacterial processes. Hardground formation, in the beginning, may also be a microbiological process, but most cementation is accomplished inorganically.
The Sis palaeovalley: a record of proximal fluvial sedimentation and drainage basin development in response to Pyrenean mountain building
Authors: Vincent Stephen J.
Published: March 2003

The Sis conglomerate body represents the Middle Eocene to Oligocene transfer‐zone trunk palaeovalley fill of the Sis fluvial system, a drainage system established within the Pyrenees during Late Palaeocene times. The spatial stability of the fluvial transfer zone (active for at least 38 My), and hence the longevity of its aggradational palaeovalley component (>19·5 My), was controlled by its location between long‐lived pre‐existing structures. Coarse‐grained fluvial facies dominate the palaeovalley fill, with alluvial fan facies shed from its defining marginal structures. The detailed sedimentology of very proximal fluvial facies deposited within the dominantly erosional realm of an active mountain belt has rarely been documented before because of their poor preservation potential. The Sis conglomerate body contains a robust internal stratigraphy with stratigraphic units defined by distinct bounding surfaces, across which there are pronounced changes in facies and provenance. These mark the reorganization of the headward portions of the Sis fluvial system during the evolution of the Pyrenean Axial Zone antiformal stack. Major changes in discharge resulted, demonstrating the highly variable nature of even mountain belt‐scale fluvial systems when viewed on timescales of several to tens of millions of years. Provenance details indicate that initial unroofing of Hercynian granitoids, situated within the Pyrenean Axial Zone, occurred around 54·5 Ma (early Ypresian) immediately before the first significant exhumation event within the drainage basin of the Sis fluvial system. This is earlier than previously constrained by apatite fission track studies. Rock uplift accelerated in the Lutetian and Bartonian with the initial aggradation of the palaeovalley fill (the Cajigar and Cornudella Formations and Sis One and Two Members). This became marked in the Priabonian (Sis Three and Four Members), with significant activity on local structures including the Morreres backthrust. An increase in basement‐derived clasts and a headwater decapitation event also indicate pronounced Axial Zone antiformal stack development at this time. Axial Zone development intensified further in the Oligocene with the deposition of the Collegats Formation and the switch in the main depositional loci of the system from the Tremp‐Graus thrust‐sheet‐top basin to the Ebro Basin to the south.
Late Pleistocene–early Holocene fluvial facies and depositional processes in the Fehmarn Belt, between Germany and Denmark, revealed by high‐resolution seismic and lithofacies analysis
Authors: Novak Bernhard , Björck Svante
Published: March 2003

In the narrow offshore border zone between Germany and Denmark, 550 km of high‐density 3·5‐kHz subbottom seismic reflection profiles were recorded within a 70‐km2 area in order to reconstruct the seismic stratigraphy of late Pleistocene to early Holocene lacustrine and fluvial environments. Using detailed line drawings, seismic facies analyses and a hierarchy of bounding surfaces, a depositional unit was recognized and subdivided into subunits 4a (oblique‐parallel), 4b (mound, oblique‐tangential), 4c (sigmoid, oblique), 4d and 4e (shingled and parallel). The base of this seismic facies association defines a wide U‐shaped valley with well‐defined scours and, in the valley sides, ‘steps’ are located above deep steep‐dipping reflections. Stratigraphic control was available from 32 coring sites (5‐ to 12‐m‐deep vibrocores). Subunit 4b represents coarsening‐up silt and sand, and samples from subunit 4d show fining‐up fine sand, silt and clay. The seismic facies association is proposed to have formed by a fluvial event of short duration some time in the period between 10·3 14C ka BP and 9·0 14C ka BP. Subunits 4a to 4e represent gradually decreasing flow power. A peak flow initiated the fluvial event, after which water discharge and level fell rapidly. Subsequently, the normal background discharge from the Baltic Sea area dominated the flow style. Reflections beneath the ‘step’‐like valley side with high dip angles are interpreted as faults. This tectonic activity resulted in subsidence in the analysed area and could possibly have influenced the fluvio‐dynamic development. The seismic stratigraphic succession reveals a high‐resolution record of sediments in this area. In particular, the stepwise uncovering of the morphology of the subunits, preserved in high‐resolution seismic facies associations, is proposed as a useful tool in modelling the dynamic development of the near sea‐floor environment.
Between beds and sequences: stratigraphic organization at intermediate scales in the Quaternary of the Virginia coast, USA
Authors: Swift Donald J. P. , Parsons Brian S. , Foyle Anthony , Oertel George F.
Published: March 2003

ABSTRACT Stratigraphy presupposes a hierarchy of scales of spatial organization supplemented at the small‐scale end by sedimentological concepts (beds, bed sets and bed cosets) and, at larger spatial scales, by sequence‐stratigraphic concepts (systems tracts, parasequences, sequences). Between these two end‐members are intermediate‐scale bodies described as ‘lithofacies’, or simply ‘facies’. A more restricted concept, granulometric facies, can be described in terms of horizontal grain‐size gradients (‘facies change’) and cyclic vertical grain‐size gradients (‘stratification’). Assemblages of facies so defined (also called depositional systems) are not random, but occur in a limited suite of patterns. Such assemblages may be linked to two classes of bounding surfaces, a source diastem (the immediate source of the sediment) and a surface of closure (if preserved), between which is sandwiched a transgressive or regressive, basinward‐fining facies succession. Systems‐bounding surfaces are notably more continuous than internal (gradational) facies boundaries. By thus restricting the definition of a facies assemblage (depositional system), it is possible to describe the Quaternary of the Virginia coast with as few as 12 systems. Depositional systems in the Quaternary of the Virginia coast are allometric, in that any system can be derived from any other by plastic expansion of one or more facies relative to another, or by simple symmetry operations. Self‐similarity prevails across this intermediate scale of stratigraphic organization. Facies assemblages (depositional systems) consist of event beds, which themselves have erosional basal boundaries and internal successions of microfacies. At larger spatial scales, depositional systems are repeated, either autocyclic repetitions forced by processes within the basin of deposition or allocyclic repetitions, as ‘parasequences’ and high‐frequency sequences. In the Virginia Quaternary, systems architecture is compatible with sequence architecture and nests conformably within its framework, but analysis of systems architecture reveals rules beyond those governing sequence architecture.
Lenomyrmex, an enigmatic new ant genus from the Neotropical Region (Hymenoptera: Formicidae: Myrmicinae)
Authors: C. Fernando Fernández , G. Edgard E. Palacio
Published: March 2003

Abstract. We describe a new myrmicine ant genus, Lenomyrmex, with four new species: L. mandibularis (type species) and L. foveolatus from Colombia, L. wardi from Ecuador and Colombia, and L. costatus from Panama. The new taxon is clearly distinguished from other myrmicine ants by the following combination of characters: (1) mandibles elongate‐triangular, with crenulate masticatory margin three times longer than basal margin, and bearing a series of ten to twenty minute peg‐like denticles that arise along and immediately behind the masticatory margin; (2) frontal lobes poorly expanded laterally, partly covering the antennal fossae; (3) large and deep antennal fossae; (4) antennal scrobes absent; (5) eyes protuberant; (6) petiole pedunculate, with poorly defined node and with an anteroventral subpetiolar process pointed anteriorly. The affinities of this new taxon within Myrmicinae remain unclear and the observed characters do not permit it to be included satisfactorily in any of the known tribes or genus groups of the subfamily.
Phylogeny of Culicomorpha (Diptera)
Authors: Sæther O. A.
Published: March 2003

The phylogeny of the families of Culicomorpha and their closest relatives are cladistically reinvestigated adding published information from several sources. A revised data matrix is presented and some characters are discussed. Different outgroups and options used, characters unordered or ordered, the results reweighted or not and the results discussed. Nymphomyiidae in all cladograms, alone or together with Thaumaleidae, forms the sister group of the traditional Culicomorpha and should be included in this infraorder as suggested by others. Superfamily Chironomoidea is not monophyletic as Thaumaleidae or Nymphomyiidae + Thaumaleidae form the sister group to the remaining traditional Culicomorpha. The mutual relationships of Chironomidae, Simuliidae and Ceratopogonidae are variable between cladograms. They form a monophyletic group with Chironomidae and Simuliidae as sister groups when characters are unordered and reweighted or when some characters are ordered, others unordered and the result reweighted. When the characters are ordered, or when a combination of ordered and unordered are used they form a Hennigian comb with the phyletic sequence Chironomidae/Ceratopogonidae/Simuliidae. When characters are ordered and reweighted the phyletic sequence is Chironomidae/Simuliidae/Ceratopogonidae. Culicoidea is monophyletic in all cladograms, but the division into superfamilies is not warranted.
A cladistic analysis of Erythracarinae (Acarina: Prostigmata: Anystidae), with the description of a new genus
Authors: Otto Jürgen C.
Published: March 2003

A cladistic analysis of sixty erythracarine species is presented and used to justify recent nomenclatorial changes to the classification of erythracarine genera. Erythracarinae is redescribed, and a new diagnosis for the subfamily and a key to the included genera are presented. Neotarsolarcus is recognized as a junior synonym of Tarsolarkus, which is recorded for the first time from North America. A new genus, Pedidromus, with six new species (P. agitatus sp.n. P. curiosus sp.n., P. durongensis sp.n., P. peliculus sp.n., P. pilotrix sp.n., P. velox sp.n.) is described.
From thickening to extension in the Variscan belt — kinematic evidence from Sardinia (Italy)
Authors: Conti P. , Carmignani L. , Oggiano G. , A.  , A.
Published: March 2003

The Variscan nappe stack of SE Sardinia originated as a result of several stages of nappe imbrication during the Lower Carboniferous phases of the Variscan orogeny. The crustal shortening caused regional SSW‐and W‐directed thrusting, greenschist facies metamorphism and open‐to‐isoclinal polyphase folding. The final stage of shortening produced large‐scale antiforms and synforms.

Post‐collisional deformation resulted in inversion of earlier thrusts as normal faults, development of low‐angle normal faults, and refolding of earlier foliation and thrust planes by asymmetric folds with subhorizontal axial planes. Facing directions of these latest folds are directed horizontally outward from the hinge zones of main antiforms, suggesting that they cannot be regarded as parasitic folds of the latest thickening phase, but instead are the consequence of vertical shortening during gravitational collapse of dome‐like km‐scale antiforms, leading to denudation of antiformal culminations.
Geochronological evidence for late‐Grenvillian magmatic and metamorphic events in central Taimyr, northern Siberia*
Authors: Pease V. , Gee D. G. , Vernikovsky V. , Vernikovskaya A. , Kireev S.
Published: March 2003

U–Th–Pb analyses of zircons from six granites and one metasediment collected in the accretionary Central belt of Taimyr, Arctic Siberia, demonstrate that Neoproterozoic (c. 900 Ma) granites intrude late Mesoproterozoic/early Neoproterozoic amphibolite facies metamorphic rocks. This is the first time in the Mamont–Shrenk region that Neoproterozoic ages have been recognized for these lithologies, previously thought to be Archaean/Palaeoproterozoic in age. The Mamont–Shrenk Terrane (MST) represents a Grenvillian age (micro?) continent intercalated with younger Neoproterozoic ophiolites during thrusting and accreted to the northern margin of the Siberian craton sometime before the late Vendian. Basement to the MST may have been derived from the Grenvillian belt of east Greenland. Viable tectonic reconstructions must allow for an active margin along northern Siberia (modern day coordinates) in the middle Neoproterozoic.
The carboxy‐terminal end of glycolate oxidase directs a foreign protein into tobacco leaf peroxisomes.
Authors: Volokita M
Published: March 2003

The carboxy‐terminal residues of several peroxisomal proteins were shown to act as a peroxisomal targetting signal. This study was conducted to test whether the C‐terminus of glycolate oxidase, a key enzyme in the glycolate metabolism pathway, is functioning as a targetting signal that directs proteins into plant leaf peroxisomes. A chimeric gene coding for a fusion protein composed of the C‐terminal‐ truncated beta‐glucuronidase, a synthetic linker of four amino acids and the last six C‐terminal amino acids of glycolate oxidase, was constructed. Transformation of tobacco plants with the chimeric gene resulted in expression of beta‐glucuronidase enzymic activity. About 50% of the transgenic beta‐glucuronidase activity was localized to the peroxisomes. The results indicate that the six C‐terminal amino acid residues of glycolate oxidase act as a targetting signal that is recognized by leaf peroxisomes.
The ptl1 gene expressed in the transmitting tissue of Antirrhinum encodes an extensin‐like protein.
Authors: Baldwin TC , Coen ES , Dickinson HG
Published: March 2003

ptl1, a gene expressed specifically in pistil transmitting tissue of Antirrhinum flowers, encodes a protein with similarity to plant extensins. The protein is rich in proline (28%) and serine (9%) and contains several proline‐rich repetitive amino acid motifs found in other extensin‐like proteins. The presence of three consensus N‐ glycosylation sites indicates that it is probably glycosylated. RNA blots show that the ptl1 transcript is abundant in mature pistillar tissue but absent from immature flower buds and all other plant organs tested. In‐situ localization of mRNA demonstrates that ptl1 expression is confined to the transmitting tissue of the style and stigma. The presence of a putative signal peptide at the N‐terminus of the protein, taken together with the expression pattern, indicates that the ptl1 product may be secreted into the extracellular matrix of the transmitting tissue. The possible contributions of the ptl1 product to the physical properties of the transmitting tissue are considered in the light of current views on extensin structure and function.
The 54 kDa RNA‐binding protein from mustard chloroplasts mediates endonucleolytic transcript 3′ end formation in vitro
Authors: Nickelsen Jörg , Link Gerhard
Published: March 2003

A 54 kDa protein from mustard chloroplasts was previously shown to interact specifically with a conserved U‐rich sequence element in RNA derived from the 3′ flanking regions of the plastid trnK and rps16 genes, which code for tRNALys and ribosomal protein CS19, respectively (Nickelsen and Link, 1991). This RNA‐binding protein has now been purified by affinity chromatography on heparin Sepharose and poly(U) Sepharose. In vitro processing experiments and nuclease S1 analyses of the processing products revealed that the 54 kDa polypeptide is an endonuclease. The in vitro cleavage sites are consistent with the positions of corresponding transcript in vivo 3′ ends downstream of trnK and rps16, suggesting that RNA 3′ end formation takes place endonucleolytically also in vivo.
Active cdc2 genes and cell cycle phase‐specific cdc2‐related kinase complexes in hormone‐stimulated alfalfa cells
Authors: Magyar Zoltán , Bakó László , Bögre László , Dedeoglu Damla , Kapros Tamás , Dudits Dénes
Published: March 2003

Hormones as auxins and cytokinins trigger the division cycle in differentiated plant cells and are required for the maintenance of proliferation in cultured cells in vitro. Northern analysis showed that the expression pattern of alfalfa cdc2 genes is significantly different in cells of primary explants exposed to hormone treatment and of rapidly cycling suspension culture. Transcription of at least one of the cdc2 genes is activated by hormones in cultured leaf mesophyll protoplasts or in root tissues treated with auxins and cytokinins. In a suspension culture of alfalfa cells, cdc2 transcripts are at a constitutively high level, irrespective of actual cell cycle phase. In addition to the transcriptional control of cdc2 genes, in hormone‐induced cells cdc2‐related kinase complexes were identified as potential phase‐specific components of post‐transcriptional regulation of the cell cycle. The known specific interaction between eukaryotic p34cdc2 protein complexes and the yeast p13suc1 protein was exploited for purification of cell cycle regulatory protein kinases from alfalfa. Alfalfa suspension cells were synchronized either for G1 phase by double‐phosphate‐starvation or for S phase by hydroxyurea treatment. The p13suc1‐Sepharose affinity matrix bound two cdc2 protein‐related complexes, one with increased histone H1 kinase activity in S, the other in G2/M phase. The complex from S phase cells showed higher kinase activity than the G2/M phase complex. Immunoblotting of p13suc1‐Sepharose‐bound protein complex showed the presence of a 33–34 kDa doublet that is recognized by anti‐PSTAIR antibodies and the co‐purification of two proteins (apparent molecular mass 65 and 42 kDa) cross‐reacting with human cyclin A antibodies. Immunoprecipitation with these cyclin A antibodies allowed the detection of a third cdc2‐related kinase complex that appeared during G1/S and early S phases of the cell cycle and phosphorylated histone H1. The results suggest that a multi‐component regulatory system is in control of the cell cycle in plants, which includes a hormone‐activated transcriptional control of cdc2 genes and phase‐specific cdc2‐related kinase complexes.
Growth‐related gene expression in Nicotiana tabacum mesophyll protoplasts
Authors: Marty Isabelle , Brugidou Christophe , Chartier Yvette , Meyer Yves
Published: March 2003

Eight cDNAs whose genes are more strongly expressed in suspension cells in growth phase than in stationary phase and at a low level in mature leaves have been isolated. The corresponding mRNAs are abundantly accumulated in young plant organs and in germinating seeds but are almost undetectable in mature plant tissues and dry seeds. Six of these cDNAs were characterized by comparison of nucleotide and protein sequences to the EMBL and SWISSPROT databanks. These eight growth‐related genes are expressed in protoplasts isolated from Nicotiana tabacum mesophyll cells shortly after preparation (4 h). Two of them are expressed in freshly isolated protoplasts (early genes), while the other six are detected after 4 h of culture (late genes). Seven are more abundantly expressed in protoplasts than in growing plant organs while one growth‐related gene is weakly expressed in protoplasts, as is the histone H4 gene. They seem to be induced in protoplasts by a synergistic effect of wounding and maceration. Sustained expression of the early genes is dependent on the presence of sucrose in the culture medium.
The Arabidopsis Athb‐2 and ‐4 genes are strongly induced by far‐red‐rich light
Authors: Carabelli Monica , Sessa Giovanna , Baima Simona , Morelli Giorgio , Ruberti Ida
Published: March 2003

The isolation and characterization of the Athb‐2 gene, which codes for a HD‐Zip protein in Arabidopsis thaliana is reported. Interestingly, Southern analysis has established that the Arabidopsis genome contains sequences which are highly related to the Athb‐2 HD‐Zip coding region. One of these genes, designated Athb‐4, has been cloned and partially sequenced. Amino acid sequence comparison revealed that Athb‐2 and −4 are members of a small family of HD‐Zip related proteins. Athb‐2 mRNA analysis showed that this gene is expressed during the vegetative and reproductive phases of plant growth. A significant increment in the amount of Athb‐2 transcripts was observed in flowering plants. A higher steady‐state level of the Athb‐2 mRNA was also found in dark‐adapted plants. Remarkably, far‐red‐rich light treatment of Arabidopsis plants results in a rapid and strong induction of the Athb‐2 expression. This light treatment also induces the accumulation of Athb‐4 transcripts, suggesting a similar role for the two members of this HD‐Zip family.
Isolation of an asparagus intracellular PR gene (AoPR1) wound‐responsive promoter by the inverse polymerase chain reaction and its characterization in transgenic tobacco
Authors: Warner Simon A. J. , Scott Rod , Draper John
Published: March 2003

The Asparagus officinalis intracellular PR1 (AoPR1) gene is expressed in response to wounding and pathogen attack. We utilized the inverse polymerase chain reaction (IPCR) to isolate the cis‐acting regulatory sequences of the AoPR1 gene following unsuccessful attempts to identify hybridizing clones in genomic libraries. Sequence analysis of two IPCR products revealed that a 347 bp intron was present in the AoPR1 gene and that it was probable that the AoPR1 regulatory sequence had been amplified. To test the AoPR1 cis‐acting sequences for biological function a translational fusion was constructed with the β‐glucuronidase (GUS) reporter gene and tested in tobacco. These data demonstrated that sequences 982 bp from the probable start of transcription are sufficient to direct wound‐inducible transcription and that there is no signal peptide encoded by the first 31 residues of the predicted AoPR1 protein. Histochemical localization of GUS activity in transgenic tobacco demonstrated strong activity localized to wound and pathogen invasion sites. GUS activity was also found in mature pollen grains.
Expression of the S‐locus receptor kinase multigene family in Brassica oleracea
Authors: Kumar Vinod , Trick Martin
Published: March 2003

The S‐receptor kinase (SRK) gene which is implicated in the self‐incompatibility system of Brassica oleracea is one member of a large and complex family of similar sequences. Genomic and cDNA clones were isolated for the authentic, S‐linked SRK29 gene and its DNA sequence determined. Reverse transcriptase PCR (RT‐PCR) was used to detect the expression of SRK,29 and other members of the family in stigma, leaf and root tissues. The SRK was found to be stigma‐specific whereas, for instance, K3 transcripts appeared in all three tissues. The RT‐PCR analysis also demonstrated the existence of partially processed intermediates for several of the kinase transcripts and, in the case of SRK29, a product apparently resulting from the splicing of a cryptic intron. RFLP analysis of an F2 family segregating for the S29 allele was used to show S‐linkage for the SRK and possibly for the K2 sequence. The K8 kinase probe also revealed a minor RFLP which segregated with the S‐locus.
Accurate in vitro transcription from circularized plasmid templates by plant whole cell extracts
Authors: Zhu Qun , Chappell Joseph , Hedrick Susan A. , Lamb Chris
Published: March 2003

A convenient in vitro transcription system using monocot and dicot whole cell extracts and circular DNA templates has been developed. The system consists of incubating template and whole cell extract to generate initiation complexes, followed by addition of nucleotide triphosphates to support elongation, and primer extension assay to detect authentic transcripts. This in vitro transcription system required circularized templates and was essentially inactive with linearized templates. Accurate in vitro transcription of a rice phenylalanine ammonia‐lyase (PAL) promoter‐β‐glucuronidase (GUS) gene fusion and a tobacco sesquiterpene cyclase promoter‐GUS gene fusion was examined in their homologous whole cell extracts, and the optimal concentrations for several reaction components, including DNA template, whole cell extract, monovalent and divalent cations, were determined for specific initiation from the in vivo start site. Transcription was inhibited by low concentrations of α‐amanitin, demonstrating that the reaction was mediated by RNA polymerase II. Accurate transcription initiation was dependent on the TATA‐box motif within the respective promoters. Based on the effect of delayed addition of sarkosyl at a concentration sufficient to inhibit transcription initiation but not elongation, three to four rounds of transcription were initiated in standard assays.
Basic plasticity of protein expression in tobacco leaf plasma membrane
Authors: Masson Florence , Rossignol Michel
Published: March 2003

Highly purified plasma membrane fractions were prepared using top‐, middle‐ or bottom‐leaf sets of tobacco. Plasma membrane polypeptides were analysed by two‐dimensional gel electrophoresis and the abundances of 90 polypeptides non‐washed out by Triton X‐100 were quantified by image analysis. Under constant environmental conditions, the relative abundances of approximately 75% of polypeptides were shown to change during plant development, irrespective of the position of the leaves on the plant. The greatest plasticity of the plasma membrane polypeptide pattern was observed, first during the early stages of plant development, including floral induction, and, to a lesser extent, during the late stages, including seed formation. Some of the leaf plasma membrane polypeptides were abundant only at specific developmental stages and in specific leaf sets. A similar situation existed during the nycthemeron, where the abundances of approximately 75% of the polypeptides were observed to change during a 24 h period. Some polypeptides appeared to be essentially dark‐ or light‐specific. Overall data analysis supports the conclusion that, under constant environmental conditions, approximately 90% of plant plasma membrane polypeptides are simultaneously subjected to both long‐term (day‐scaled) and short‐term (hour‐scaled) dynamics. This unexpected steady‐state dynamics (i) corresponds to a new kind of plasticity which has to be distinguished from the phenotypic plasticity shown by plants in response to various changes in environmental factors, (ii) provides new insights into the functioning of membranes and is proposed to constitute a signature of the plant physiological state.
The intravacuolar organic matrix associated with calcium oxalate crystals in leaves of Vitis
Authors: Webb Mary Alice , Cavaletto John M. , Carpita Nicholas C. , Lopez Linda E. , Arnott Howard J.
Published: March 2003

In Vitis (grape) calcium oxalate crystals form in a needle‐like morphology unique to plants, presenting an intriguing system of biological control over mineral formation. Crystals develop within an organic matrix which appears to provide control over the sites and forms of crystal deposition; however, little is known about the chemical nature of the matrix. A procedure has been developed to isolate crystals along with their associated intravacuolar matrix from leaves of grape, and studies have been initiated into the chemical composition of the matrix by characterizing elemental content, carbohydrates, and protein. The isolated matrix consisted of two structural phases, membrane chambers enclosing developing crystals, and a water‐soluble phase surrounding the crystal chambers. Elemental analysis detected substantial calcium and potassium, as well as some iron in the water‐soluble phase. Analysis of the water‐soluble matrix by GC‐MS showed that it contained an unusual polymer with novel glucuronic acid linkages. In addition, linkage analysis indicated 5‐linked arabinans, arabinogalactan, and various mannosyl units typical of complex carbohydrates of N‐linked glycoproteins. SDS—PAGE analysis of the water‐soluble matrix and crystal chambers showed that each had distinct banding profiles in silver‐stained gels, with prominent 60 and 70 kDa polypeptides in crystal chamber extracts. Demineralization studies provided direct evidence that the isolated matrix promotes crystal nucleation. The findings about the organic matrix associated with calcium oxalate crystals in grape are discussed in relation to crystal nucleation and growth and features shared with animal and microbial biomineralization systems.
Mapping of branchpoint nucleotides in mutant pre‐mRNAs expressed in plant cells
Authors: Liu Hong‐Xiang , Filipowicz Witold
Published: March 2003

Pre‐mRNA encoding rubisco activase in the Arabidopsis thaliana mutant rca contains a GU to AU change at the 5′ splice site of intron 3 and this mutation results in accumulation of splicing intermediates bearing an incompletely processed intron. It has been demonstrated that one of the intermediates contains intron 3 in the form of a lariat and the branchpoint nucleotide has been mapped to the A residue at position −32 forming part of the sequence UUGAU. Analysis of a similar GU to AU 5′ splice site mutation, present in a synthetic pre‐mRNA context expressed in transfected protoplasts of Nicotiana plumbaginifolia, also suggests formation of lariats with branching occurring at A−31. A small fraction (approximately 10%) of this mutant pre‐mRNA also underwent the second step of splicing. In addition to the consensus AG, an AU dinucleotide was used as splicing acceptor.
Protease‐sensitive thylakoidal import machinery for the Sec‐, ΔpH‐ and signal recognition particle‐dependent protein targeting pathways, but not for CFoII integration
Authors: Robinson David , Karnauchov Ivan , Herrmann Reinhold G. , Klösgen Ralf Bernd , Robinson Colin
Published: March 2003

Nuclear‐encoded proteins are targeted into and across the thylakoid membrane by a surprising variety of mechanisms. Distinct Sec‐ and ΔpH‐dependent mechanisms have been shown to operate for lumenal proteins, and an integral membrane protein, LHCP, has been shown to insert via a signal recognition particle‐dependent route. Integration of a further membrane protein, CFoII, requires neither soluble factors nor energy sources, prompting speculation of a spontaneous insertion mechanism. Although the requirements for soluble factors and energy sources have been determined in some detail, much less is known of the events taking place at the membrane surface. This report examines whether thylakoid proteins are involved in each of these pathways, by testing the effects of trypsin on the capacity of isolated thylakoids to import proteins. Because all of the pathways rely to some extent on the thylakoidal ΔpH, and a light‐induced ΔpH is easily destroyed by proteolysis, the conditions under which reverse action of the ATP synthase in the dark generates a high ΔpH even after proteolysis of thylakoids have been established. This system is used to show that protease‐sensitive thylakoidal import machinery is crucial for the ΔpH‐, Sec‐ and signal recognition particle‐dependent pathways, but not for integration of CFoII.
The NADH‐binding subunit of respiratory chain complex I is nuclear‐encoded in plants and identified only in mitochondria
Authors: Grohmann Lutz , Rasmusson Allan G. , Heiser Volker , Thieck Oliver , Brennicke Axel
Published: March 2003

In higher plants, genes for subunits of respiratory chain complex I (NADH:ubiquinone oxidoreductase) have so far been identified solely in organellar genomes. At least nine subunits are encoded by the mitochondrial DNA and 11 homologues by the plastid DNA. One of the ‘key’ components of complex I is the subunit binding the substrate NADH. The corresponding gene for the mitochondrial subunit has now been cloned and identified in the nuclear genome from potato (Solanum tuberosum). The mature protein consists of 457 amino acids and is preceded by a mitochondrial targeting sequence of 30 amino acids. The protein is evolutionarily related to the NADH‐binding subunits of complex I from other eukaryotes and is well conserved in the structural domains predicted for binding the substrate NADH, the FMN and one iron‐sulphur cluster. Expression examined in different potato tissues by Northern blot analysis shows the highest steady‐state mRNA levels in flowers.

Precursor proteins translated in vitro from the cDNA are imported into isolated potato mitochondria in a ΔΨ‐dependent manner. The processed translation product has an apparent molecular mass of 55 kDa, identical to the mature protein present in the purified plant mitochondrial complex I. However, the in‐vitro translated protein is not imported into isolated chloroplasts. To further investigate whether the complex I‐like enzyme in chloroplasts contains an analogous subunit for binding of NAD(P)H, different plastid protein fractions were tested with a polyclonal antiserum directed against the bovine 51 kDa NADH‐binding subunit. In none of the different thylakoid or stroma protein fractions analysed were specific crossreactive polypeptides detected. These results are discussed particularly with respect to the structure of a potential complex I in chloroplasts and the nature of its acceptor site.
Isolation and characterization of a cDNA encoding mitochondrial chaperonin 10 from Arabidopsis thaliana by functional complementation of an Escherichia coli groES mutant
Authors: Koumoto Yasuko , Tsugeki Ryuji , Shimada Tomoo , Mori Hitoshi , Kondo Maki , Hara‐Nishimura Ikuko , Nishimura Mikio
Published: March 2003

Chaperonin (Cpn) is one of the molecular chaperones. Cpn10 is a co‐factor of Cpn60, which regulates Cpn60‐mediated protein folding. It is known that Cpn10 is located in mitochondria and chloroplasts in plant cells. The Escherichia coli homologue of Cpn10 is called GroES. A cDNA for the Cpn10 homologue was isolated from Arabidopsis thaliana by functional complementation of the E. coli groES mutant. The cDNA was 647 bp long and encoded a polypeptide of 98 amino acids. The deduced amino acid sequence showed approximately 50% identity to mammalian mitochondrial Cpn10s and 30% identity to GroES. A Northern blot analysis revealed that the mRNA for the Cpn10 homologue was expressed uniformly in various organs and was markedly induced by heat‐shock treatment. The Cpn10 homologue was constitutively expressed in transgenic tobaccos. Immunogold and immunoblot analyses following the subcellular fractionation of leaves from transgenic tobaccos revealed that the Cpn10 homologue was localized in mitochondria and accumulated at a high level in transgenic tobaccos.