bluuebunny/crossref_metadata_2025 huggingface dataset:
Terminal deoxynucleotidyltransferase is negatively regulated by direct interaction with proliferating cell nuclear antigen
Authors: Ibe Shirou , Fujita Kiyoko , Toyomoto Tsuguri , Shimazaki Noriko , Kaneko Reo , Tanabe Akiko , Takebe Izumi , Kuroda Sachiko , Kobayashi Tamami , Toji Shingo , Tamai Katsuyuki , Yamamoto Hiroko , Koiwai Osamu
Published: March 2003

Background The repertoires of Ig and TcR are generated by a combinatorial rearrangement of variable (V), diversity (D), and joining (J) segments (V(D)J recombination) in B‐ and T‐cells. Terminal deoxynucleotidyltransferase (TdT) adds extra nucleotides (N nucleotides) at the junctions of the gene segments to enhance the Ig and TcR genes diversity. Using an anti‐TdT antibody column, TdT has been purified as a member of a megadalton protein complex from rat thymus. The N region would be synthesized with the large protein complex.

Results The cDNAs for proliferating cell nuclear antigen (PCNA) were isolated by yeast two‐hybrid screening as the gene products which directly interacted with TdT. The interaction between PCNA and TdT was confirmed by co‐immunoprecipitation, both in vitro and in vivo. TdT binds directly to a PCNA trimer, as shown by gel filtration. TdT interacts with PCNA in its DNA polymerization domain (DPD), but not in its BRCA‐1 C‐terminal (BRCT) domain. TdT activity was reduced to 17% of the maximum value by TdT/PCNA complex formation.

Conclusion TdT interacts directly with PCNA through its DPD. A functional consequence of this interaction is the negative regulation of TdT activity. These findings suggest that TdT catalyses the addition of N nucleotides under the negative control of PCNA during V(D)J recombination.
The RGS domain‐containing fission yeast protein, Rgs1p, regulates pheromone signalling and is required for mating
Authors: Pereira Paulo S. , Jones Nic C.
Published: March 2003

Background When nutritionally starved, the fission yeast Schizosaccharomyces pombe enters a cell differentiation process which leads to mating and meiosis. The Ste11 protein is a key regulator of this differentiation pathway, activating the transcription of mating and meiotic genes upon starvation.

Results Here, we describe rgs1, a member of the Regulator of G‐protein Signalling (RGS) family, as a novel Ste11 target gene. rgs1 expression requires both an Ste11‐mediated nitrogen starvation signal and the pheromone‐induced activation of the Byr2/Byr1/Spk1 MAPK pathway. We show that rgs1 deletion results in a sensitivity to pheromone and in a mating defect. Δrgs1 cells initiate the mating pathway normally, undergoing sexual agglutination and G1 arrest, while inducing pheromone‐dependent transcription, but then fail to fuse with a mating partner while elongating abnormal conjugation tubes. Endogenous Rgs1 tagged with GFP localizes to the nucleus and cytoplasm, and this localization pattern is not altered during pheromone treatment. Importantly, Rgs1 function requires its C‐terminal RGS domain, as well as a central DEP domain and a novel homology domain present in its N‐terminal region (Fungal‐DR domain).

Conclusions These results demonstrate that rgs1 expression requires nutritional starvation and pheromone signalling. Rgs1 negatively regulates pheromone signalling during mating, acting in a negative feedback loop that is essential for the mating process.
Mammalian homologue of E. coli ras‐like GTPase (ERA) is a possible apoptosis regulator with RNA binding activity
Authors: Akiyama Taishin , Gohda Jin , Shibata Saiko , Nomura Yukiko , Azuma Sakura , Ohmori Yoshihiro , Sugano Sumio , Arai Hiroyuki , Yamamoto Tadashi , Inoue Jun‐ichiro
Published: March 2003

Background ERA (Escherichia coliRas‐like protein) is an E. coli GTP binding protein that is essential for proliferation. A DNA database search suggests that homologous sequences with ERA exist in various organisms including human, mouse, Drosophila, Caenorhabditis elegans and Antirrhinum majus. However, the physiological function of eukaryotic ERA‐like proteins is not known.

Results We have cloned cDNAs encoding the entire coding region of a human homologue (H‐ERA) and a mouse homologue (M‐ERA) of ERA. The mammalian homologue of ERA consists of a typical GTPase/GTP‐binding domain and a putative K homology (KH) domain, which is known as an RNA binding domain. We performed transfection experiments with wild‐type H‐ERA or various H‐ERA mutants. H‐ERA possessing the amino acid substitution mutation into the GTPase domain induced apoptosis of HeLa cells, which was blocked by Bcl‐2 expression. Deletion of the C‐terminus, which contains a part of the KH domain, alleviated apoptosis by the H‐ERA mutant, suggesting the importance of this domain in the function of H‐ERA. We have also shown the RNA binding activity of H‐ERA by pull‐down experiments using RNA homopolymer immobilized on beads or recombinant H‐ERA proteins.

Conclusion Our data suggest that H‐ERA plays an important role in the regulation of apoptotic signalling with its GTPase/GTP binding domain.
Nucleocytoplasmic transport of proteins and poly(A)+ RNA in reconstituted Tpr‐less nuclei in living mammalian cells
Authors: Shibata Satoshi , Matsuoka Yosuke , Yoneda Yoshihiro
Published: March 2003

Background: It is known that Tpr is a component of an intranuclear long filament which extends from the nuclear pore complex (NPC) into the nucleoplasm. Since the over‐expression of the full‐length of or some fragments of Tpr in living cells leads to the accumulation of poly(A)+ RNA within the nuclei, it is generally thought that a relationship exists between Tpr and the nuclear export of mRNA in mammalian cells. In contrast, the nuclear export of poly(A)+ RNA was not inhibited in a double deletion mutant of yeast Tpr homologues (Mlp1p and Mlp2p). Therefore, the precise function of Tpr remains unknown.

Results: By microinjecting two types of polyclonal antibodies which are specific to Tpr into the cytoplasm of living mammalian interphase cells, we succeeded in reconstituting the Tpr‐less nuclei. In the Tpr‐less nuclei, the localization of the major components of the NPC, the nuclear import of SV40 T‐NLS substrates and the nuclear export of HIV Rev NES‐substrates were not affected. However poly(A)+ RNA accumulated in the non‐snRNP splicing factor SC35‐positive clusters, which became larger in size and fewer in number, compared with normal nuclei.

Conclusion: These results indicate that Tpr plays a critical role in the intranuclear dynamics of RNA pol II transcripts, including the processing, intranuclear transport and targeting, as well as their translocation through the NPC in mammalian cells.
Involvement of NLK and Sox11 in neural induction in Xenopus development
Authors: Hyodo‐Miura Junko , Urushiyama Seiichi , Nagai Shin‐ichi , Nishita Michiru , Ueno Naoto , Shibuya Hiroshi
Published: March 2003

Background : The Wnt signal transduction pathway regulates various aspects of embryonal development and has been implicated in promoting cancer. Signalling by Wnts leads to the stabilization of cytosolic β‐catenin, which then associates with TCF transcription factors to regulate expression of Wnt‐target genes. The Wnt pathway is further subject to cross‐regulation at various levels by other components.

Results: Recent evidence suggests that a specific MAP kinase pathway involving the MAP kinase kinase kinase TAK1 and the MAP kinase NLK counteract Wnt signalling. In particular, it has been shown that TAK1 activates NLK, which phosphorylates TCFs bound to β‐catenin. This phosphorylation down‐regulates the DNA‐binding activity of a TCF‐4/β‐catenin complex, and blocks activation of their target genes. To investigate the role of NLK in Xenopus development, we isolated xNLK, a Xenopus homologue of NLK. Our findings indicate that xNLK is expressed in neural tissues and induces the anterior‐neural marker gene, Otx‐2. Moreover, xSox11, which is induced by the expression of Chordin, co‐operates with xNLK to induce neural development. These molecules also interact in mammalian cells, and expression of a mutant of xNLK lacking kinase activity was found to suppress the induction of neural marker gene expression by xSox11.

Conclusions : Our findings indicate that xNLK may play a role in neural development together with xSox11 during early Xenopus embryogenesis.
Spectral imaging fluorescence microscopy
Authors: Haraguchi Tokuko , Shimi Takeshi , Koujin Takako , Hashiguchi Noriyo , Hiraoka Yasushi
Published: March 2003

The spectral resolution of fluorescence microscope images in living cells is achieved by using a confocal laser scanning microscope equipped with grating optics. This capability of temporal and spectral resolution is especially useful for detecting spectral changes of a fluorescent dye; for example, those associated with fluorescence resonance energy transfer (FRET). Using the spectral imaging fluorescence microscope system, it is also possible to resolve emitted signals from fluorescent dyes that have spectra largely overlapping with each other, such as fluorescein isothiocyanate (FITC) and green fluorescent protein (GFP).
Functional domains of paired‐like homeoprotein Cart1 and the relationship between dimerization and transcription activity
Authors: Furukawa Keizo , Iioka Takashi , Morishita Mariko , Yamaguchi Akira , Shindo Hiroyuki , Namba Hiroyuki , Yamashita Shunichi , Tsukazaki Tomoo
Published: March 2003

Background: Cart1 encodes the paired‐like homeodomain in the central portion of the gene, and plays a crucial role in the developmental lineage of bone and cartilage, especially in head formation. However, its transactivation mechanism is still poorly understood, including the target gene. Here, we report biochemical dissections of Cart1 functional domains and a relationship between dimerization and transcription activity.

Results: Deletion studies of GAL4‐fused Cart1 indicated that the transactivation domain is located in the middle portion of the C‐terminal domain, but the N‐terminal is also required for a full activation of the consensus palindromic binding site (TAATNNNATTA). Analysis of the basic amino acid residues at both ends of the homeodomain revealed that both sides act as nuclear localization signals, and are necessary for the cooperative binding to the palindromic sequence. In this study, two additional Cart1 isoforms that behave as dominant negatives were identified from rat chondrosarcoma cells. These isoforms suppressed the transcription activity of the wild‐type, despite loss of DNA binding ability, and could interact with the wild‐type in yeast. Finally, we demonstrated that wild‐type Cart1 forms a DNA‐independent homodimer in in vivo conditions, and that the transactivation of wild‐type Cart1 was suppressed by the N‐ or C‐terminal domain which was expressed in the nucleus.

Conclusion: These results revealed that homodimerization through direct interaction is necessary for the potent transcription activity of Cart1.
Roles of aurora‐A kinase in mitotic entry and G2 checkpoint in mammalian cells
Authors: Marumoto Tomotoshi , Hirota Toru , Morisaki Tetsuro , Kunitoku Naoko , Zhang Dongwei , Ichikawa Yasuko , Sasayama Takashi , Kuninaka Shinji , Mimori Tatsuyuki , Tamaki Norihiko , Kimura Masashi , Okano Yukio , Saya Hideyuki
Published: March 2003

Background: Various mitotic events are controlled by Cdc2‐cyclin B and other mitotic kinases. Aurora/Ipl1‐related mitotic kinases were proved to play key roles in mitotic progression in diverse lower organisms. Aurora‐A is a mammalian counterpart of aurora/Ipl1‐related kinases and is thought to be a potential oncogene. However, the regulation of aurora‐A activation and the commitment of aurora‐A in the progression of G2‐M phase are largely unknown in mammalian cells.

Results: We demonstrated that aurora‐A is activated depending on the activation of Cdc2‐cyclin B in mammalian cells. Since Cdc2‐cyclin B does not directly phosphorylate aurora‐A, indirect pathways such as the inhibition of PP1 by Cdc2‐cyclin B may act for the activation of aurora‐A kinase. Microinjection of anti‐aurora‐A antibodies into HeLa cells at late G2 phase caused a significant delay in mitotic entry. Furthermore, aurora‐A activation at G2‐M transition was inhibited by DNA damage, and the over‐expression of aurora‐A induced the abrogation of the DNA damage‐induced G2 checkpoint.

Conclusions: Aurora‐A is activated downstream of Cdc2‐cyclin B and plays crucial roles in proper mitotic entry and G2 checkpoint control. Dysregulation of aurora‐A induces abnormal G2‐M transition in mammalian cells and may lead to chromosome instability, which results in the development and progression of malignant tumours.
Signalling mechanisms in sphingosine 1‐phosphate‐promoted mesangial cell proliferation
Authors: Katsuma Susumu , Hada Yuko , Ueda Toshihiro , Shiojima Satoshi , Hirasawa Akira , Tanoue Akito , Takagaki Kazuchika , Ohgi Tadaaki , Yano Junichi , Tsujimoto Gozoh
Published: March 2003

Background: The bioactive sphingolipid sphingosine 1‐phosphate (S1P) is formed by the activation of sphingosine kinase (SPHK) in diverse stimuli, such as platelet‐derived growth factor (PDGF). S1P acts not only as an extracellular mediator but also as an intracellular second messenger, resulting in the proliferation of various different types of cells. However, the signal transduction mechanism in S1P‐induced proliferation of mesangial cells is poorly known.

Results: We examined the signalling mechanisms by which S1P and dihydro‐S1P (DHS1P), another S1P receptor agonist, induce mesangial cell proliferation. We first observed that exogenous S1P/DHS1P had additive effects on the PDGF‐promoted proliferation of mesangial cells. Treatment of mesangial cells with pertussis toxin almost completely inhibited S1P‐ and DHS1P‐induced, and slightly inhibited PDGF‐induced cell proliferation. Additionally, the ERK kinase inhibitor PD98059 partially blocked the proliferation of mesangial cells induced by all these ligands. N,N‐dimethylsphingosine, a competitive inhibitor of SPHK, reduced PDGF‐induced mesangial cell proliferation, whereas over‐expression of SPHK promoted it. We also revealed that PDGF induces SPHK mRNA expression and SPHK activity, suggesting that SPHK, which links the PDGF to the S1P signalling cascade, is, at least in part, involved in PDGF‐induced mesangial cell proliferation. Moreover, we found that extracellular S1P stimulates two S1P receptors, EDG3 and EDG5, which leads to cell proliferation and survival.

Conclusions: The data show that S1P‐induced mesangial cell proliferation is mediated by EDG‐dependent and ‐independent signalling pathways. S1P may cooperate with PDGF to increase the proliferation of mesangial cells during pathophysiological processes.
Thrombopoietin‐induced CXC chemokines, NAP‐2 and PF4, suppress polyploidization and proplatelet formation during megakaryocyte maturation
Authors: Oda Masaaki , Kurasawa Yasuhiro , Todokoro Kazuo , Nagata Yuka
Published: March 2003

Background:  We previously reported that the expressions of two CXC chemokines, neutrophil activating peptide‐2 (NAP‐2) and platelet factor‐4 (PF‐4), were induced by megakaryocyte‐specific cytokine thrombopoietin (TPO) in mouse bone marrow megakaryocytes. The roles of these chemokines on megakaryocyte maturation/differentiation processes, including polyploidization and proplatelet formation (PPF) remain unresolved.

Results:  NAP‐2 and PF‐4 suppressed the PPF of mature megakaryocytes freshly prepared from mouse bone marrow as well as that of the megakaryocyte progenitors, c‐Kit+CD41+ cells, isolated from mouse bone marrow and cultured with TPO. NAP‐2 and PF‐4 inhibited polyploidization of c‐Kit+CD41+ cells in the presence of TPO, and also inhibited the proliferation of c‐Kit+CD41+ cells.

Conclusions:  NAP‐2 and PF‐4 produced by TPO stimulation in megakaryocytes suppress megakaryocyte maturation and proliferation as a feedback control.
Antagonistic and agonistic effects of an extracellular fragment of nectin on formation of E‐cadherin‐based cell‐cell adhesion
Authors: Honda Tomoyuki , Shimizu Kazuya , Kawakatsu Tomomi , Yasumi Masato , Shingai Tatsushi , Fukuhara Atsunori , Ozaki‐Kuroda Kumi , Irie Kenji , Nakanishi Hiroyuki , Takai Yoshimi
Published: March 2003

Background: Nectin is a Ca2+‐independent immunoglobulin‐like cell‐cell adhesion molecule at the E‐cadherin‐based cell‐cell adherens junctions (AJs), and comprises a family consisting of four members, nectin‐1, ‐2, ‐3, and ‐4. Nectin and E‐cadherin are associated with afadin and α‐catenin, actin filament (F‐actin)‐binding proteins connecting respective adhesion molecules to the actin cytoskeleton, but the role of nectin in the formation of the E‐cadherin‐based cell‐cell AJs has not yet been fully understood. To obtain evidence for this role of nectin, we attempted to develop an antagonist and/or agonist of nectin.

Results: We made a recombinant extracellular fragment of nectin‐3 (Nef‐3). Nef‐3 trans‐interacted with cellular nectin‐1 and thereby diminished the formation of the nectin‐1‐based cell‐cell adhesion. This resulted in a reduction of the formation of the E‐cadherin‐based cell‐cell adhesion in L fibroblasts stably expressing both exogenous nectin‐1α and E‐cadherin (nectin‐1‐EL cells) and MDCK cells stably expressing exogenous nectin‐1α (nectin‐1‐MDCK cells). This antagonistic effect of Nef‐3 was also observed in L cells stably expressing exogenous E‐cadherin alone (EL cells) and wild‐type MDCK cells. Conversely, Nef‐3 coated on microbeads first recruited the nectin–afadin complex and then the E‐cadherin–catenin complex to the bead‐cell contact sites in nectin‐1‐EL and nectin‐1‐MDCK cells.

Conclusion: These results suggest that nectin is necessary and sufficient for the recruitment of E‐cadherin to the nectin‐based cell‐cell adhesion sites and involved in the formation of E‐cadherin‐based cell‐cell AJs.
Micrometeorites: Little rocks with a big message
Authors: GENGE MATTHEW
Published: March 2003

Solar systems come to us
Geological monuments on the South Banke
Authors: ROBINSON ERIC
Published: March 2003

An urban geological tour
A geology of the road
Authors: Robinson Eric
Published: March 2003

Before the Roman came to Rye or out to Severn strode,

The rolling English drunkard made the rolling English road.
Mineralogical composition of atmospheric airborne particulates
Authors: Williamson B. J.
Published: March 2003

A massive increase in public concern in the last 20 years about the health effects of atmospheric airborne particulates has caused a surge in research activities and has led to ever more stringent government air‐quality standards.
Did elephants hang from trees? – the giant sloths of South America
Authors: Bell C. M.
Published: March 2003

One hundred years ago, the discovery of fresh‐looking, red, hairy skin and huge piles of dung of an extinct animal caused a media storm. The remains were found jumbled with human bones and tools on the floor of a cave near the southern tip of South America. Were the huge, cumbersome, hamster‐like creatures known as ground sloths still roaming the remote forests?
Processing, modelling and predicting time-lapse effects of overpressured fluid-injection in a fractured reservoir
Authors: Angerer Erika , Crampin Stuart , Li Xiang-Yang , Davis Thomas L.
Published: March 2003

Time-lapse seismology is important for monitoring subsurface pressure changes and fluid movements in producing hydrocarbon reservoirs. We analyse two 4-D, 3C onshore surveys from Vacuum Field, New Mexico, USA, where the reservoir of interest is a fractured dolomite. In Phase VI, a time-lapse survey was acquired before and after a pilot tertiary-recovery programme of overpressured CO2 injection, which altered the fluid composition and the pore-fluid pressure. Phase VII was a similar time-lapse survey in the same location but with a different lower-pressure injection regime.

Applying a processing sequence to the Phase VI data preserving normal-incidence shear-wave anisotropy (time-delays and polarization) and maximizing repeatability, interval-time analysis of the reservoir interval shows a significant 10 per cent change in shear-wave velocity anisotropy and 3 per cent decrease in the P-wave interval velocities. A 1-D model incorporating both saturation and pressure changes is matched to the data. The saturation changes have little effect on the seismic velocities. There are two main causes of the time-lapse changes. Any change in pore-fluid pressures modifies crack aspect ratios. Additionally, when there are overpressures, as there are in Phase VI, there is a 90° change in maximum impedance directions, and the leading faster split shear wave, instead of being parallel to the crack face as it is for low pore-fluid pressures, becomes orthogonal to the crack face. The anisotropic poro-elasticity (APE) model of the evolution of microcracked rock, calculates the evolution of cracked rock to changing conditions. APE modelling shows that at high overburden pressures only nearly vertical cracks, to which normal incidence P waves are less sensitive than S waves, remain open as the pore-fluid pressure increases. APE modelling matches the observed time-lapse effects almost exactly demonstrating that shear-wave anisotropy is a highly sensitive diagnostic of pore-fluid pressure changes in fractured reservoirs.

In this comparatively limited analysis, APE modelling of fluid-injection at known pressure correctly predicted the changes in seismic response, particularly the shear-wave splitting, induced by the high-pressure CO2 injection. In the Phase VII survey, APE modelling also successfully predicted the response to the lower-pressure injection using the same Phase VI model of the cracked reservoir. The underlying reason for this remarkable predictability of fluid-saturated reservoir rocks is the critical nature and high crack density of the fluid-saturated cracks and microcracks in the reservoir rock, which makes cracked reservoirs critical systems.
Data and model uncertainty estimation for linear inversion
Authors: Kasper van Wijk , John A Scales , William Navidi , Luis Tenorio
Published: March 2003

Inverse theory concerns the problem of making inferences about physical systems from indirect noisy measurements. Information about the errors in the observations is essential to solve any inverse problem, otherwise it is impossible to say when a feature ‘fits the data’. In practice, however, one seldom has a direct estimate of the data errors. We exploit the trade-off between data prediction and model or data structure to determine both model-independent and modelbased estimates of the noise characteristics from a single realization of the data. Noise estimates are then used to characterize the set of reasonable models that fit the data, for example, by bintersecting prior model parameter constraints with the set of data fitting models. This prior information can also be used to set bounds on the bias.We illustrate our methods with synthetic examples of vertical seismic profiling and cross-well tomography.
Seismic and ultrasonic velocities in permafrost
Authors: Carcione José M. , Seriani Géza
Published: March 2003

We calculate the compressional‐ and shear‐wave velocities of permafrost as a function of unfrozen water content and temperature. Unlike previous theories based on simple slowness and/or moduli averaging or two‐phase models, we use a Biot‐type three‐phase theory that considers the existence of two solids (solid and ice matrices) and a liquid (unfrozen water). The compressional velocity for unconsolidated sediments obtained with this theory is close to the velocity computed with Wood's model, since Biot's theory involves a Wood averaging of the moduli of the single constituents. Moreover, the model gives lower velocities than the well‐known slowness averaging theory (Wyllie's equation). For consolidated Berea sandstone, the theory underestimates the value of the compressional velocity below 0°C. Computing the average bulk moduli by slowness averaging the ice and solid phases and Wood averaging the intermediate moduli with the liquid phase yields a fairly good fit of the experimental data. The proportion of unfrozen water and temperature are closely related. Fitting the wave velocity at a given temperature allows the prediction of the velocity at the whole range of temperatures, provided that the average pore radius and its standard deviation are known.
Fracture‐frequency prediction from borehole wireline logs using artificial neural networks
Authors: FitzGerald Elaine M. , Bean Christopher J. , Reilly Ronan
Published: March 2003

Borehole‐wall imaging is currently the most reliable means of mapping discontinuities within boreholes. As these imaging techniques are expensive and thus not always included in a logging run, a method of predicting fracture frequency directly from traditional logging tool responses would be very useful and cost effective. Artificial neural networks (ANNs) show great potential in this area. ANNs are computational systems that attempt to mimic natural biological neural networks. They have the ability to recognize patterns and develop their own generalizations about a given data set. Neural networks are trained on data sets for which the solution is known and tested on data not previously seen in order to validate the network result. We show that artificial neural networks, due to their pattern recognition capabilities, are able to assess the signal strength of fracture‐related heterogeneity in a borehole log and thus fracture frequency within a borehole. A combination of wireline logs (neutron porosity, bulk density, P‐sonic, S‐sonic, deep resistivity and shallow resistivity) were used as input parameters to the ANN. Fracture frequency calculated from borehole televiewer data was used as the single output parameter. The ANN was trained using a back‐propagation algorithm with a momentum learning function. In addition to fracture frequency within a single borehole, an ANN trained on a subset of boreholes in an area could be used for prediction over the entire set of boreholes, thus allowing the lateral correlation of fracture zones.
Analysis of Thomsen parameters for finely layered VTI media
Authors: Berryman James G. , Grechka Vladimir Y. , Berge Patricia A.
Published: March 2003

Since the work of Postma and Backus, much has been learned about elastic constants in vertical transversely isotropic (VTI) media when the anisotropy is due to fine layering of isotropic elastic materials. Nevertheless, there has continued to be some uncertainty about the possible range of Thomsen's anisotropy parameters ε and δ for such media. We use both Monte Carlo studies and detailed analysis of Backus' equations for both two‐ and three‐component layered media to establish the results presented. We show that ε lies in the range −3/8  ε  ½[〈v2p〉〈v−2p〉−1], for finely layered media; smaller positive and all negative values of ε occur for media with large fluctuations in the Lamé parameter λ in the component layers. We show that δ can also be either positive or negative, and that for constant density media, sign (δ) = sign (〈v−2p〉 − 〈v−2s〉〈v2s/v2p〉). Monte Carlo simulations show that among all theoretically possible random media, positive and negative δ are equally likely in finely layered media. (Of course, the δs associated with real earth materials may span some smaller subset of those that are theoretically possible, but answering this important question is beyond our present scope.) Layered media having large fluctuations in λ are those most likely to have positive δ. This is somewhat surprising since ε is often negative or a small positive number for such media, and we have the general constraint that ε − δ > 0 for layered VTI media. Since Gassmann's results for fluid‐saturated porous media show that the mechanical effects of fluids influence only the Lamé parameter λ, not the shear modulus μ, these results suggest that small positive δ occurring together with small positive ε (but somewhat larger than δ) may be indicative of changing fluid content in a layered earth.
Inversion of normal moveout for monoclinic media1
Authors: Grechka Vladimir , Contreras Pedro , Tsvankin Ilya
Published: March 2003

Multiple vertical fracture sets, possibly combined with horizontal fine layering, produce an equivalent medium of monoclinic symmetry with a horizontal symmetry plane. Although monoclinic models may be rather common for fractured formations, they have hardly been used in seismic methods of fracture detection due to the large number of independent elements in the stiffness tensor. Here, we show that multicomponent wide‐azimuth reflection data (combined with known vertical velocity or reflector depth) or multi‐azimuth walkaway VSP surveys provide enough information to invert for all but one anisotropic parameters of monoclinic media.

In order to facilitate the inversion procedure, we introduce a Thomsen‐style parametrization for monoclinic media that includes the vertical velocities of the P‐wave and one of the split S‐waves and a set of dimensionless anisotropic coefficients. Our notation, defined for the coordinate frame associated with the polarization directions of the vertically propagating shear waves, captures the combinations of the stiffnesses responsible for the normal‐moveout (NMO) ellipses of all three pure modes. The first group of the anisotropic parameters contains seven coefficients (ε(1,2), δ(1,2,3) and γ(1,2)) analogous to those defined by Tsvankin for the higher‐symmetry orthorhombic model. The parameters ε(1,2), δ(1,2) and γ(1,2) are primarily responsible for the pure‐mode NMO velocities along the coordinate axes x1 and x2 (i.e. in the shear‐wave polarization directions). The remaining coefficient δ(3) is not constrained by conventional‐spread reflection traveltimes in a horizontal monoclinic layer. The second parameter group consists of the newly introduced coefficients ζ(1,2,3) which control the rotation of the P‐, S1‐ and S2‐wave NMO ellipses with respect to the horizontal coordinate axes. Misalignment of the P‐wave NMO ellipse and shear‐wave polarization directions was recently observed on field data by Pérez et al.

Our parameter‐estimation algorithm, based on NMO equations valid for any strength of the anisotropy, is designed to obtain anisotropic parameters of monoclinic media by inverting the vertical velocities and NMO ellipses of the P‐, S1‐ and S2‐waves. A Dix‐type representation of the NMO velocity of mode‐converted waves makes it possible to replace the pure shear modes in reflection surveys with the PS1‐ and PS2‐waves. Numerical tests show that our method yields stable estimates of all relevant parameters for both a single layer and a horizontally stratified monoclinic medium.
Azimuth‐dependent AVO in reservoirs containing non‐orthogonal fracture sets
Authors: Sayers Colin M. , Dean Simon
Published: March 2003

Azimuthal anisotropy in rocks can result from the presence of one or more sets of partially aligned fractures with orientations determined by the stress history of the rock. The symmetry of a rock with horizontal bedding that contains two or more non‐orthogonal sets of vertical fractures may be approximated as monoclinic with a horizontal plane of mirror symmetry. For offsets that are small compared with the depth of the reflector, the azimuthal variation in P‐wave AVO gradient for such a medium varies with azimuth as where φ is the azimuth measured with respect to the fast polarization direction for a vertically polarized shear wave. φ2 depends on both the normal compliance BN and the shear compliance BT of the fractures and may differ from zero if BNBT varies significantly between fracture sets. If BNBT is the same for all fractures,

and the principal axes of the azimuthal variation in P‐wave AVO for fixed offset are determined by the polarization directions of a vertically propagating shear wave. At larger offsets, terms in

and

are required to describe the azimuthal variation in AVO accurately. φ4 and φ6 also depend on BNBT. For gas‐filled open fractures

but a lower value of BNBT may result from the presence of a fluid with non‐zero bulk modulus.
The 3D shear experiment over the Natih field in Oman: the effect of fracture‐filling fluids on shear propagation
Authors: Van Der Kolk C.M. , Guest W.S. , Potters J.H.H.M.
Published: March 2003

This is the final paper in a series on the 3D multicomponent seismic experiment in Oman. In this experiment a 3D data set was acquired using three‐component geophones and with three source orientations. The data set will subsequently be referred to as the Natih 9C3D data set. We present, for the first time, evidence demonstrating that shear waves are sensitive to fluid type in fractured media. Two observations are examined from the Natih 9C3D data where regions of gas are characterized by slow shear‐wave velocities. One is that the shear‐wave splitting map of the Natih reservoir exhibits much larger splitting values over the gas cap on the reservoir. This increase in splitting results from a decrease in the slow shear‐wave velocity which senses both the fractures and the fracture‐filling fluid. Using a new effective‐medium model, it was possible to generate a splitting map for the reservoir that is corrected for this fluid effect. Secondly, an anomaly was encountered on the shear‐wave data directly above the reservoir. The thick Fiqa shale overburden exhibits a low shear‐wave velocity anomaly that is accompanied by higher shear reflectivity and lower frequency content. No such effects are evident in the conventional P‐wave data. This feature is interpreted as a gas chimney above the reservoir, a conclusion supported by both effective‐medium modelling and the geology.

With this new effective‐medium model, we show that introduction of gas into vertically fractured rock appears to decrease the velocity of shear waves (S2), polarized perpendicular to the fracture orientation, whilst leaving the vertical compressional‐wave velocity largely unaffected. This conclusion has direct implications for seismic methods in exploration, appraisal and development of fractured reservoirs and suggests that here we should be utilizing S‐wave data, as well as the conventional P‐wave data, as a direct hydrocarbon indicator.
Seismic refraction, isotropic anisotropic seismic tomography on an ancient monument (Antonino and Faustina temple ad 141)
Authors: Cardarelli Ettore , De Nardis Rita
Published: March 2003

This paper describes the results of using geophysical techniques to investigate three columns of the Pronaos of the Antonino and Faustina temple (AD 141) in Rome, Italy; the columns are of cipollino marble which shows alternate sequences of mica and calcite beds. We applied seismic refraction using traditional interpretation, and seismic transmission tomography. The comparison between the results of the refraction study and the 2D and 3D isotropic tomographic analyses suggested anisotropic characteristics for the marble, and this prompted us to perform a further tomographic experiment, taking into account these characteristics of the material. Assuming an elliptical model, the main directions of anisotropy were detected. Two velocity fields corresponding to the main directions of the anisotropy were measured and anomalies such as cracks and fractures were noted. The conjugate‐gradient algorithm was used to invert the data. The results of the isotropic and anisotropic models were compared. The correlation between the methods highlighted the characteristics of the marble, i.e. anisotropy, depth of the weathering, fractures and small cracks. The results show that the material of the columns is in reasonable condition, with the exception of a surface area 6 cm to 15 cm deep that we estimate has been weathered for 2000 years, and that has been particularly affected by pollution in the last century.
Numerical viscoelastic modelling by the spectral Laguerre method
Authors: Mikhailenko B.G. , Mikhailov A.A. , Reshetova G.V.
Published: March 2003

Seismic wave propagation in a viscoelastic media can be described by a system of integro‐differential equations. The solution of such equations requires special methods when using finite‐difference techniques in the time domain. In the frequency domain, the integral terms are represented by complex elastic parameters. This paper presents an efficient algorithm for viscoelastic modelling based on the integral Laguerre transform for the approximation of temporal derivatives and for the calculation of convolution integrals. For the calculation of spatial derivatives, it is possible to use various methods: finite‐difference and finite‐element techniques, spectral and pseudo‐spectral methods. We then obtain a system of algebraic equations with a matrix independent of the parameter m, i.e. the degree of the Laguerre polynomials. In this case, only the right‐hand side of the system has recurrent dependence on the parameter m, which is an analogue of the temporal frequency in the frequency domain. The obtained system with a large number of right‐hand sides can be solved using fast methods, where the matrix is transformed only once, as opposed to the frequency‐domain approach, when the matrix is transformed for each temporal frequency.
Free Air CO2 Enrichment of potato (Solanum tuberosum L.): development, growth and yield
Authors: Miglietta F. , Magliulo V. , Bindi M. , Cerio L. , Vaccari F. P. , Loduca V. , Peressotti A.
Published: March 2003

A FACE (Free Air CO2 Enrichment) experiment was carried out on Potato (Solanum tuberosum L., cv. Primura) in 1995 in Italy. Three FACE rings were used to fumigate circular field plots of 8 m diameter while two rings were used as controls at ambient CO2 concentrations. Four CO2 exposure levels were used in the rings (ambient, 460, 560 and 660 μmol mol–1). Phenology and crop development, canopy surface temperature, above‐ and below‐ground biomass were monitored during the growing season. Crop phenology was affected by elevated CO2, as the date of flowering was progressively anticipated in the 660, 560, 460 μmol mol–1 treatments. Crop development was not affected significantly as plant height, leaf area and the number of leaves per plant were the same in the four treatments. Elevated atmospheric CO2 levels had, instead, a significant effect on the accumulation of total nonstructural carbohydrates (TNC = soluble sugars + starch) in the leaves during a sunny day. Specific leaf area was decreased under elevated CO2 with a response that paralleled that of TNC concentrations. This reflected the occurrence of a progressive increase of photosynthetic rates and carbon assimilation in plants exposed to increasingly higher levels of atmospheric CO2. Tuber growth and final tuber yield were also stimulated by rising CO2 levels. When calculated by regression of tuber yield vs. the imposed levels of CO2concentration, yield stimulation was as large as 10% every 100 μmol mol–1 increase, which translated into over 40% enhancement in yield under 660 μmol mol–1. This was related to a higher number of tubers rather than greater mean tuber mass or size. Leaf senescence was accelerated under elevated CO2 and a linear relationship was found between atmospheric CO2 levels and leaf reflectance measured at 0.55 μm wavelength. We conclude that significant CO2 stimulation of yield has to be expected for potato under future climate scenarios, and that crop phenology will be affected as well.
Effects of environment during growth on the sensitivity of leaf conductance to changes in humidity
Authors: Bunce James A.
Published: March 2003

Soybeans (Glycine max) and grain amaranth (Amaranthus hypochondriacus) were grown at a range of temperatures, carbon dioxide concentrations and light conditions in controlled environment chambers, and the response of leaf conductance to water vapour to changes in humidity was then measured under a standard set of conditions. The sensitivity of conductance was analysed in terms of (i) the absolute sensitivity of conductance to changes in leaf to air water vapour pressure difference (LAVPD), (ii) the sensitivity of conductance relative to the absolute value of conductance, and (iii) the slope of the relationship between conductance and an index incorporating assimilation rate, carbon dioxide concentration and relative humidity. The sensitivity of conductance varied substantially with growth conditions for all three analyses in both species. The growth temperature of 25 °C increased the sensitivity of conductance by all three measures compared with growth at 20 or 30 °C in amaranth, with little difference between 25 and 30 °C in soybean. Growth at elevated carbon dioxide decreased sensitivity in amaranth by all three measures, and decreased the absolute but not the relative sensitivity in soybean. Growth at reduced photon flux density and growth at high stand density reduced sensitivity in amaranth by all three measures. In soybean, growth at high stand density reduced sensitivity by all three measures, but growth at low photon flux density increased the relative sensitivity. The sensitivity of leaf conductance to changes in humidity varied by a factor of two or more with growth environment by all measures of sensitivity in both the C3 and the C4 species.
Methane emission by termites and oxidation by soils, across a forest disturbance gradient in the Mbalmayo Forest Reserve, Cameroon
Authors: Macdonald Jannette A. , Eggleton PauL. , Bignell David E. , Forzi Francis , Fowler David
Published: March 2003

Methane fluxes were measured, using static chambers, across a disturbance gradient in a West African semi‐deciduous humid forest. Soil‐feeding termite biomass was simultaneously determined, in an attempt to examine its influence on the net soil‐atmosphere exchange of CH4. CH4 emission rates from individual termite species were determined under laboratory conditions, permitting the gross production of CH4 to be compared with net fluxes to the atmosphere. Both net CH4 oxidation(‐) and emission were observed, and CH4 fluxes ranged from – 24.6 to 40.7 ng m–2 s–1. A statistically significant relationship between termite biomass and CH4 flux was observed across the forested sites such that: CH4 flux (ng m–2 s–1) = 4.95 × termite biomass (gm–2)–10.9 (P < 0.001). Rates of CH4 oxidation were on average 60% smaller at the clearfelled and Terminalia plantation sites than at the near‐primary forest site. Two of the disturbed sites were net CH4 sources during one of the sampling periods. Disturbance of tropical forests, resulting in a decrease in the CH4 sink capacity of the soil, may therefore increase the contribution of termite‐derived CH4 to the atmosphere. Measurements from the mounds of the soil‐feeding termites Thoracotermes macrothorax and Cubitermes fungifaber from the old plantation site gave a CH4 emission of 636 and 53.4 ng s–1 mound–1, respectively. The forest floor surrounding the mounds was sampled in three concentric bands. Around the mound of T. macrothorax the soil was a net source of CH4 estimated to contribute a further 148 ng s–1. Soil surrounding the mound of C. fungifaber was mostly a net sink. The mounds of soil‐feeding termites are point sources of CH4, which at the landscape scale may exceed the general sink capacity of the soil, to an extent dependent on seasonal variations in soil moisture and level of disturbance.
The implications of predicted climate change for insect pests in the UK, with emphasis on non‐indigenous species
Authors: CANNON RAYMOND J. C.
Published: March 2003

Recent estimates for global warming predict increases in global mean surface air temperatures (relative to 1990) of between 1 and 3.5 °C, by 2100. The impact of such changes on agricultural systems in mid‐ to high‐latitude regions are predicted to be less severe than in low‐latitude regions, and possibly even beneficial, although the influence of pests and diseases is rarely taken into account. Most studies have concluded that insect pests will generally become more abundant as temperatures increase, through a number of inter‐related processes, including range extensions and phenological changes, as well as increased rates of population development, growth, migration and over‐wintering. A gradual, continuing rise in atmospheric CO2will affect pest species directly (i.e. the CO2fertilization effect) and indirectly (via interactions with other environmental variables). However, individual species responses to elevated CO2vary: consumption rates of insect herbivores generally increase, but this does not necessarily compensate fully for reduced leaf nitrogen. The consequent effects on performance are strongly mediated via the host species. Some recent experiments under elevated CO2have suggested that aphids may become more serious pests, although other studies have discerned no significant effects on sap‐feeding homopterans. However, few, if any of these experiments have fully considered the effects on pest population dynamics. Climate change is also considered from the perspective of changes in the distribution and abundance of species and communities. Marked changes in the distribution of well‐documented species – including Odonata, Orthoptera and Lepidoptera – in north‐western Europe, in response to unusually hot summers, provide useful indications of the potential effects of climate change. Migrant pests are expected to respond more quickly to climate change than plants, and may be able to colonize newly available crops/habitats. Range expansions, and the removal of edge effects, could result in the increased abundance of species presently near the northern limits of their ranges in the UK. However, barriers to range expansions, or shifts, may include biotic (competition, predation, parasitism and disease), as well as abiotic, factors. Climatic phenomena, ecosystem processes and human activities are interactive and interdependent, making long‐term predictions extremely tenuous. Nevertheless, it appears prudent to prepare for the possibility of increases in the diversity and abundance of pest species in the UK, in the context of climate change.
Microbial community structure and global trace gases
Authors: SCHIMEL JOSHUA P. , GULLEDGE JAY.
Published: March 2003

Global change can affect soil processes by either altering the functioning of existing organisms or by restructuring the community, modifying the fundamental physiologies that drive biogeochemical processes. Thus, not only might process rates change, but the controls over them might also change. Moreover, previously insignificant processes could become important. These possibilities raise the question ‘Will changes in climate and land use restructure microbial communities in a way that will alter trace gas fluxes from an ecosystem?’ Process studies indicate that microbial community structure can influence trace gas dynamics at a large scale. For example, soil respiration and CH4 production both show ranges of temperature response among ecosystems, indicating differences in the microbial communities responsible. There are three patterns of NH4+ inhibition of CH4 oxidation at the ecosystem scale: no inhibition, immediate inhibition, and delayed inhibition; these are associated with different CH4 oxidizer communities. Thus, it is possible that changes in climate, land‐use, and disturbance regimes could alter microbial communities in ways that would substantially alter trace gas fluxes; we discuss the data supporting this conclusion. We also discuss approaches to developing research linking microbial community structure and activity to the structure and functioning of the whole ecosystem. Modern techniques allow us to identify active organisms even if they have not been cultivated; in combination with traditional experimental approaches we should be able to identify the linkages between these active populations and the processes they carry out at the ecosystem level. Finally, we describe scenarios of how global change could alter trace gas fluxes by altering microbial communities and how understanding the microbial community dynamics could improve our ability to predict future trace gas fluxes.