bluuebunny/crossref_metadata_2025 huggingface dataset:
Translation ability of mitochondrial tRNAsSer with unusual secondary structures in an in vitro translation system of bovine mitochondria
Authors: Hanada Takao , Suzuki Tsutomu , Yokogawa Takashi , Takemoto‐Hori Chie , Sprinzl Mathias , Watanabe Kimitsuna
Published: March 2003

Background Metazoan mitochondrial (mt) tRNAs are structurally quite different from the canonical cloverleaf secondary structure. The mammalian mt tRNASerGCU for AGY codons (Y = C or U) lacks the entire D arm, whereas tRNASerUGA for UCN codons (N = A, G, C or U) has an extended anti‐codon stem. It has been a long‐standing problem to prove experimentally how these tRNAsSer work in the mt translation system.

Results To solve the above‐mentioned problem, we examined their translational abilities in an in vitro bovine mitochondrial translation system using transcripts of altered tRNASer analogues derived from bovine mitochondria. Both tRNASer analogues had almost the same ability to form ternary complexes with mt EF‐Tu and GTP. The D‐arm‐lacking tRNASer GCU analogue had considerably lower translational activity than the tRNASerUGA analogue and produced mostly short oligopeptides, up to a tetramer. In addition, tRNASerGCU analogue was disfavoured by the ribosome when other tRNAs capable of decoding the cognate codon were available.

Conclusion Both mt tRNASerGCU and tRNASerUGA analogues with unusual secondary structure were found to be capable of translation on the ribosome. However, the tRNASerGCU analogue has some molecular disadvantage on the ribosome, which probably derives from the lack of a D arm.
A GyrB‐GyrA fusion protein expressed in yeast cells is able to remove DNA supercoils but cannot substitute eukaryotic topoisomerase II
Authors: Trigueros Sonia , Roca Joaquim
Published: March 2003

Background: Type II topoisomerases are a highly conserved class of enzymes which transport one double‐stranded DNA segment through a transient break in another. Whereas the eukaryotic enzymes are homodimers of a single polypeptide, their bacterial homologues are homodimers of two independently coded protein subunits. Unlike eukaryotic topoisomerase II and bacterial topoisomerase IV, DNA gyrase is a bacterial type II topoisomerase which specializes in intramolecular DNA transport.

Results: We have fused the Escherichia coli coding sequences for the proteins GyrB and GyrA, which comprise DNA gyrase. This fusion was expressed in yeast cells and yielded the expected full‐length protein product. When it was expressed in Δtop1‐ top2‐4 yeast cells, the fusion protein compensated their slow growth and reverted their elevated chromosomal excision of ribosomal genes. Furthermore, it removed DNA positive supercoils. The fusion protein, however, was unable to complement the temperature‐dependent lethality of top2‐4 cells.

Conclusion:

Fusion of the E. coli GyrB and GyrA proteins leads to a catalytically active topoisomerase which compensates several phenotypic traits attributed to unconstrained DNA supercoiling in topoisomerase‐deficient cells. However, since the fusion protein cannot substitute for topoisomerase II, it may be efficient in intramolecular but not intermolecular DNA passage, resembling the catalytic properties of DNA gyrase.
CLC‐3 deficiency leads to phenotypes similar to human neuronal ceroid lipofuscinosis
Authors: Yoshikawa Momono , Uchida Shinichi , Ezaki Junji , Rai Tatemitsu , Hayama Atsushi , Kobayashi Katsuki , Kida Yujiro , Noda Masaki , Koike Masato , Uchiyama Yasuo , Marumo Fumiaki , Kominami Eiki , Sasaki Sei
Published: March 2003

Background: CLC‐3 is a member of the CLC chloride channel family and is widely expressed in mammalian tissues. To determine the physiological role of CLC‐3, we generated CLC‐3‐deficient mice (Clcn3–/–) by targeted gene disruption.

Results: Together with developmental retardation and higher mortality, the Clcn3–/– mice showed neurological manifestations such as blindness, motor coordination deficit, and spontaneous hyperlocomotion. In histological analysis, the Clcn3–/– mice showed a pattern of progressive degeneration of the retina, hippocampus and ileal mucosa, which resembled the phenotype observed in cathepsin D knockout mice. The defect of cathepsin D results in a lysosomal accumulation of ceroid lipofuscin containing the mitochondrial F1F0 ATPase subunit c. In immunohistochemistry and Western blot analysis, we found that the subunit c was heavily accumulated in the lysosome of Clcn3–/– mice. Furthermore, we detected an elevation in the endosomal pH of the Clcn3–/– mice.

Conclusions: These results indicated that the neurodegeneration observed in the Clcn3–/– mice was caused by an abnormality in the machinery which degrades the cellular protein and was associated with the phenotype of neuronal ceroid lipofuscinosis (NCL). The elevated endosomal pH could be an important factor in the pathogenesis of NCL.
Sexually dimorphic expression of Dax‐1 in the adrenal cortex
Authors: Mukai Tokuo , Kusaka Masatomo , Kawabe Ken , Goto Kiminobu , Nawata Hajime , Fujieda Kenji , Morohashi Ken‐ichirou
Published: March 2003

Background: The DAX‐1 (also known as AHC) gene encodes an unusual member of the nuclear receptor superfamily, and the gene product plays a pivotal role during gonadal and adrenal differentiation. Mutations of the human DAX‐1 gene cause X‐linked adrenal hypoplasia congenita associated with hypogonadotropic hypogonadism. However, the molecular mechanisms underlying the transcriptional regulation of the gene are not well understood.

Results: Sexually dimorphic expression of Dax‐1 (NR0B1) in the adrenal cortex was observed by RT‐PCR, Western blotting and immunohistochemistry. The differential expression was abolished by gonadectomy and was restored again by sex steroid replacement. Our results suggested that the Dax‐1 gene transcription is suppressed by androgens and androgen receptor (AR/NR3C4). Dax‐1 gene transcription is regulated by Ad4BP/SF‐1 (NR5A1), therefore we investigated the functional correlation between A4BP/SF‐1 and AR. Interestingly, AR down‐regulated the Dax‐1 gene transcription mediated by Ad4BP/SF‐1 in the presence of the ligand. DNA binding by AR was not essential for the suppressive action, however the suppression seemed to be dependent on the promoter contexts. An interaction between Ad4BP/SF‐1 and AR was detected in the presence of the ligand for AR.

Conclusion: The present study revealed that the expression of Dax‐1 in the adrenal cortex is regulated by androgen and the receptor. Interestingly, AR acts as a suppressor in the presence of the ligand through interaction with Ad4BP/SF‐1.
Distinct roles of SOX2, Pax6 and Maf transcription factors in the regulation of lens‐specific δ1‐crystallin enhancer
Authors: Muta Mayumi , Kamachi Yusuke , Yoshimoto Aki , Higashi Yujiro , Kondoh Hisato
Published: March 2003

Background: The eye lens provides a good model for the study of regulation of cell differentiation, in which lens‐specific δ1‐crystallin expression serves as an indicator of the differentiated state of the cells. It has been indicated that the SOX2, Pax6 and Maf proteins are the major regulators of lens cell differentiation. To clarify the individual roles of these transcription factors, we analysed their participation in regulation of the δ1‐crystallin enhancer.

Results: We defined the major binding sites of SOX2, Pax6 and Maf transcription factors in the δ1‐crystallin enhancer and assessed the effect of mutations at these sites in the cultured lens epithelial cells and in developing lenses of transgenic mouse embryos. SOX2 (or SOX1/SOX3) is essential for activation of the enhancer under all conditions. Pax6 bound at the δEF3 site is required for activation of the enhancer, while Pax6 at the Pax6U site appears to be involved in the Pax6‐dependent suppression of the enhancer. In contrast, Maf proteins are only required for high enhancer activity in lens fibre cells.

Conclusion: The distinct roles of these transcription factors in the regulation of δ1‐crystallin enhancer would tend to indicate their individual functions in lens differentiation. The activity of SOX2 and the related SOX1/3 is essential at all stages of lens development as transcriptional activators. Pax6, although it is required in all steps, probably exerts complex regulatory effects, since it possesses both the potential to activate and repress. The major function of Maf proteins presumably resides in the activation of the genes in lens fibre cells.
Novel family of CCCH‐type zinc‐finger proteins, MOE‐1, ‐2 and ‐3, participates in C. elegans oocyte maturation
Authors: Shimada Masumi , Kawahara Hiroyuki , Doi Hirofumi
Published: March 2003

Background: Oocyte maturation is an important prerequisite for the production of progeny. Although several germ‐line mutations have been reported, the precise mechanism by which the last step of oocyte maturation is controlled remains unclear. In Caenorhabditis elegans, CCCH‐type zinc‐finger proteins have been shown to be involved in germ cell formation, although their involvement in oocyte maturation has not been fully investigated.

Results: Using a multiple RNAi technique, we have identified three novel redundant CCCH‐type zinc‐finger genes, named by us moe‐1, ‐2 (oma‐1, ‐2) and moe‐3, as a group related by functions and nucleotide sequence. Although a single RNAi of each moe gene was not effective, double or triple RNAi induced defects in oocyte maturation. We found that each moe transcript was expressed from the distal to proximal region of the gonad, while their corresponding proteins are accumulated exclusively in proximal oocytes, with a close association to germ granules. Although MOE‐2 protein is rapidly removed from germ granules after fertilization, we found that MOE‐2 associates with the centrosome‐peripheral structure in dividing blastomeres.

Conclusions: Our results suggest that moe gene products are unique multifunctional proteins in terms of their redundancy and characteristic behaviour during the course of oocyte maturation. These gene products participate in processes in the final step of the meiotic cell cycle control, a novel function for CCCH‐type zinc‐finger family proteins thus far discovered.
Suppression of NF‐κB‐dependent gene expression by a hexamethylene bisacetamide‐inducible protein HEXIM1 in human vascular smooth muscle cells
Authors: Ouchida Rika , Kusuhara Masatoshi , Shimizu Noriaki , Hisada Tetsuya , Makino Yuichi , Morimoto Chikao , Handa Hiroshi , Ohsuzu Fumitaka , Tanaka Hirotoshi
Published: March 2003

Background: Neointima formation is a characteristic feature of atherosclerosis and post‐angioplasty restenosis, in which various soluble factors and mechanical injury stimulate signalling pathways in vascular smooth muscle cells (VSMC), promoting their migration and proliferation, and the eventual formation of the neointima. The transcription factor NF‐κB has been shown to play a pivotal role in this process. Hexamethylene bisacetamide, an inhibitor of VSMC proliferation, induces the mRNA expression of HEXIM1 (hexamethylene bisacetamide‐inducible protein 1). However, the protein expression and function of HEXIM1 remain unknown.

Results: In the present study, we demonstrated that HEXIM1 localizes in the cytoplasm and nucleus, and its nuclear expression is restricted to discrete speckled areas. Treatment of VSMC with hexamethylene bisacetamide up‐regulated HEXIM1 expression, not only in mRNA but also protein levels. Moreover, HEXIM1 is shown to suppress the transcriptional activity of NF‐κB via its C‐terminal leucine‐rich domain. A glutathione‐S‐transferase pull down assay indicated that HEXIM1 interacts with the p65 subunit of NF‐κB. In VSMC, treatment with hexamethylene bisacetamide resulted in a down‐modulation of the transcription of NF‐κB target genes.

Conclusion: We may therefore conclude that HEXIM1 plays an inhibitory role in NF‐κB‐dependent gene expression in VSMC and is the candidate of a novel therapeutic target for inhibition of VSMC proliferation.
CDK‐ and Cdc45‐dependent priming of the MCM complex on chromatin during S‐phase in Xenopus egg extracts: possible activation of MCM helicase by association with Cdc45
Authors: Masuda Taro , Mimura Satoru , Takisawa Haruhiko
Published: March 2003

Background: MCM and Cdc45 are required for the initiation and elongation stages of eukaryotic DNA replication. Recent studies show that a purified Mcm4/6/7 complex has DNA helicase activity. However, the biochemical function of the MCM complex and Cdc45 bound to chromatin has not been elucidated.

Results: We have examined the biochemical properties of MCM proteins bound to chromatin fractions using Xenopus egg extracts. Immunoprecipitation of MCM proteins extracted under denaturing conditions reveals that all six subunits of MCM and Cdc45 form a tight complex following the initiation of DNA replication, and that both CDK activity and Cdc45 are essential for the complex formation. Chromatin immunoprecipitation of MCM proteins and Cdc45 shows that a complex containing MCM and Cdc45 has a DNA helicase activity which is dependent on CDK activity and Cdc45 in the extracts. Furthermore, both the complex and the helicase activity are resistant to treatment with phosphatase and high salt.

Conclusions: Following the initiation of DNA replication, a tight MCM–Cdc45 complex is formed on chromatin and its formation is closely correlated with the DNA helicase activity of chromatin immunoprecipitates containing MCM and Cdc45. We propose that the tight MCM–Cdc45 complex functions as a replicative DNA helicase in vivo.
PML‐nuclear bodies are involved in cellular serum response
Authors: Matsuzaki Kazuhito , Minami Takeshi , Tojo Masahide , Honda Yoshiomi , Saitoh Noriko , Nagahiro Shinji , Saya Hideyuki , Nakao Mitsuyoshi
Published: March 2003

Background: Serum stimulation leads to the activation of various signal transduction pathways in cells, and the resultant signals are integrated into the serum response factor (SRF)‐dependent transcription of immediate‐early genes such as c‐fos.

Results: To further characterize this response, we investigated the mechanism which controls serum response transcription in cultured human cells. Frequency of PML (promyelocytic leukaemia)‐nuclear bodies (NBs) formation increases shortly after serum stimulation, probably facilitating the interaction of SRF and CBP acetyltransferase at the NBs. PML modulates SRF‐mediated c‐fos promoter activities upon addition of serum to cells or expression of constitutively active Rho family GTPases. We mapped the region in the SRF that interacts with PML to the C‐terminal transactivation domain. An SRF mutant deleted of the transactivation domain neither co‐localizes with CBP in NBs nor fulfills its transcriptional role. Under conditions of serum stimulation, the formation of NBs coincides with the immediate‐early expression of the endogenous c‐fos gene in fibroblasts and in all‐trans retinoic acid‐treated acute promyelocytic leukaemia NB4 cells.

Conclusion: These data provide an insight into the involvement of NBs in modulating the transcription of serum‐induced immediate‐early genes.
Electrical resistivity tomography survey for delineating uncharted mine galleries in West Bengal, India*
Authors: Maillol J.M. , Seguin M.‐K. , Gupta O.P. , Akhauri H.M. , Sen N.
Published: March 2003

The history of subsidence, fires, flooding and other kinds of environmental hazards related to shallow coal workings in India goes back to colonial times some 300 years ago. As coal production accelerated in modern times, so did the environmental and socio‐economic drawbacks related to exploitation. In the mid‐1980s, a hydropneumatic sand‐stowing method was developed to fill in abandoned galleries but their exact location had to be known. Unfortunately, most of these old workings are uncharted and consequently large tracts of land cannot be stabilized. A research programme making use of integrated surface, borehole and cross‐hole geophysical methods was undertaken over a five‐year span to try to solve this problem. Surface geophysical methods, being cheaper and faster than their cross‐ and downhole counterparts, were used to cover larger areas on an exploratory basis, while cross‐hole methods were employed to locate more accurately one or a network of galleries to be perforated by drillhole(s) and used as a conduit for sand stowing.

We report the results of one of the cross‐hole geophysical methods: electrical resistivity tomography (ERT). A pole–dipole configuration is used and both cross‐hole and surface‐borehole methodologies are tested. Forward modelling and inversion of synthetic data making use of downhole and surface physical and geometrical parameters are presented first. This phase is followed by the inversion of real data. It is concluded that ERT is not applicable for the detection of dry voids, but is effective in a waterlogged environment which is estimated to represent 85–90% of the cases. In waterlogged galleries, ERT is applicable in both cross‐hole and surface‐downhole modes, the latter allowing a larger surface coverage at low cost. ERT is thus a reliable geophysical tool to image water‐filled voids and an adequate technique to address environmental and geotechnical problems.
Gravity changes and natural gas extraction in Groningen
Authors: Van Gelderen Martin , Haagmans Roger , Bilker Mirjam
Published: March 2003

Gravity observations made over the Groningen gasfield from 1978 onwards are available. The existing gravity data were reanalysed and a new survey was carried out. The observed gravity changes obtained during four surveys, spanning an 18‐year period, were compared with the gravity effect due to natural gas extraction computed from the reservoir model and the production data. The random error in the gravity values is small enough to detect the effect of gas extraction after a few years (up to 2 μgal/year). The trends obtained from observed and calculated gravity changes agree well within their expected error margins after statistical data snooping. Due to the inadequate measurement set‐up of the previous surveys, systematic errors present in the gravity data hampered the use of this data for refinement of the reservoir and the production models. However, with improved gravity monitoring, in particular a very systematic network set‐up and well‐calibrated instruments, this should now be feasible. By using the network analysis from the 1996 measurements for the planning of a network in space and time, most of the current problems can be avoided.
Artificial neural networks for parameter estimation in geophysics
Authors: Calderón‐Macías Carlos , Sen Mrinal K. , Stoffa Paul L.
Published: March 2003

Artificial neural systems have been used in a variety of problems in the fields of science and engineering. Here we describe a study of the applicability of neural networks to solving some geophysical inverse problems. In particular, we study the problem of obtaining formation resistivities and layer thicknesses from vertical electrical sounding (VES) data and that of obtaining 1D velocity models from seismic waveform data. We use a two‐layer feedforward neural network (FNN) that is trained to predict earth models from measured data. Part of the interest in using FNNs for geophysical inversion is that they are adaptive systems that perform a non‐linear mapping between two sets of data from a given domain. In both of our applications, we train FNNs using synthetic data as input to the networks and a layer parametrization of the models as the network output. The earth models used for network training are drawn from an ensemble of random models within some prespecified parameter limits. For network training we use the back‐propagation algorithm and a hybrid back‐propagation–simulated‐annealing method for the VES and seismic inverse problems, respectively. Other fundamental issues for obtaining accurate model parameter estimates using trained FNNs are the size of the training data, the network configuration, the description of the data and the model parametrization. Our simulations indicate that FNNs, if adequately trained, produce reasonably accurate earth models when observed data are input to the FNNs.
The effectiveness of azimuthal apparent‐resistivity measurements as a method for determining fracture strike orientations
Authors: Busby J.P.
Published: March 2003

Azimuthal apparent‐resistivity measurements are made for the purpose of determining the strike direction of subvertical fracture sets. Data are collected about a common centre, with an electrode array expanded along a sufficient number of azimuths to define the variation of apparent resistivity with orientation. The apparent resistivities for any one electrode spacing are then plotted in a polar diagram. If the data form an ellipse, this is often interpreted as reflecting aligned, subvertical fracturing. However, it is also possible for heterogeneity within the rockmass to manifest itself, at the scale of the measurement, as a variation of apparent resistivity with azimuth. It is recommended that the offset Wenner array is used for all measurements and that a parameter is introduced, the homogeneity index, which defines whether the variations due to homogeneous anisotropy, such as subvertical fracturing, are greater than those due to inhomogeneity. This simple parameter, which is the quotient of two standard deviations, is valid for both single‐peaked and multiple‐peaked ellipses. A four‐stage scheme for the interpretation of azimuthal data is suggested and a consistent set of quantitative measures is recommended. These will allow data, collected by different workers over different lithologies, to be compared. There are a number of geological situations which can give rise to anisotropy within the rockmass and great care is needed when interpreting azimuthal data in terms of aligned fracturing. Numerical modelling of the response to a buried channel of a rotated offset Wenner array demonstrates that elliptical data are generated by such a linear feature. Depending on the location of the array with respect to the channel, these data are either indistinguishable from those generated by aligned fracturing, or can be recognized by application of the homogeneity index. In the case where the response can be identified as being due to a channel, diagnostic information can be derived on the location and strike of the channel.
3D adaptive tomography using Delaunay triangles and Voronoi polygons
Authors: Böhm Gualtiero , Galuppo Paolo , Vesnaver Aldo
Published: March 2003

The solutions of traveltime inversion problems are often not unique because of the poor match between the raypath distribution and the tomographic grid. However, by adapting the local resolution iteratively, by means of a singular value analysis of the tomographic matrix, we can reduce or eliminate the null space influence on our earth image: in this way, we get a much more reliable estimate of the velocity field of seismic waves. We describe an algorithm for an automatic regridding, able to fit the local resolution to the available raypaths, which is based on Delaunay triangulation and Voronoi tessellation. It increases the local pixel density where the null space energy is low or the velocity gradient is large, and reduces it elsewhere. Consequently, the tomographic image can reveal the boundaries of complex objects, but is not affected by the ambiguities that occur when the grid resolution is not adequately supported by the available raypaths.
Robust inversion of vertical electrical sounding data using a multiple reweighted least‐squares method
Authors: Porsani Milton J. , Niwas Sri , Ferreira Niraldo R.
Published: March 2003

The root cause of the instability problem of the least‐squares (LS) solution of the resistivity inverse problem is the ill‐conditioning of the sensitivity matrix. To circumvent this problem a new LS approach has been investigated in this paper. At each iteration, the sensitivity matrix is weighted in multiple ways generating a set of systems of linear equations. By solving each system, several candidate models are obtained. As a consequence, the space of models is explored in a more extensive and effective way resulting in a more robust and stable LS approach to solving the resistivity inverse problem. This new approach is called the multiple reweighted LS method (MRLS). The problems encountered when using the L1‐ or L2‐norm are discussed and the advantages of working with the MRLS method are highlighted. A five‐layer earth model which generates an ill‐conditioned matrix due to equivalence is used to generate a synthetic data set for the Schlumberger configuration. The data are randomly corrupted by noise and then inverted by using L2, L1 and the MRLS algorithm. The stabilized solutions, even though blurred, could only be obtained by using a heavy ridge regression parameter in L2‐ and L1‐norms. On the other hand, the MRLS solution is stable without regression factors and is superior and clearer. For a better appraisal the same initial model was used in all cases. The MRLS algorithm is also demonstrated for a field data set: a stable solution is obtained.
Increasing the vertical resolution of conventional sub‐bottom profilers by parametric equalization
Authors: Cobo P. , Ranz C. , Cervera M.
Published: March 2003

Vertical resolution, i.e. the ability to resolve two close reflectors, is a crucial aspect of pulses used in geo‐acoustic exploration of sea sub‐bottoms. This paper deals with the problem of exploring the shallowest unconsolidated layers of the seafloor with conventional piezo‐electric sonar pulses. Such transducers do not have a sufficiently broad transmission response to enable them to radiate short high‐resolution pulses. Therefore, some kind of equalization process must be applied to broaden the transmission response. Here, inverse filtering is used to calculate the transducer driving waveform so that the subsequent acoustic pulse has a zero‐phase cosine‐magnitude nature. Within a specified bandwidth, this pulse has minimum length, i.e. maximum resolution.

The method has been applied to compress the acoustic pulses radiated by two piezo‐electric transducers. In conventional performance, these transducers radiate narrowband pulses which contain several cycles at the natural resonance frequency. Under equalized driving, both transducers emit broadband pulses, with resolving power greatly increased, at the cost of some amplitude loss. That is, the pulses radiated by both transducers have been shortened from 1 ms (low‐frequency transducer) and 0.274 ms (high‐frequency transducer) in conventional performance to 0.13 ms and 0.038 ms in equalized mode, with amplitude losses of 33% and 56%, respectively. The great improvement in the resolution of this technique is demonstrated by comparing the synthetic echograms that should be obtained when exploring a wedge model using zero‐phase cosine‐magnitude pulses with conventional ping pulses.
Traveltime computation with the linearized eikonal equation for anisotropic media
Authors: Alkhalifah Tariq
Published: March 2003

A linearized eikonal equation is developed for transversely isotropic (TI) media with a vertical symmetry axis (VTI). It is linear with respect to perturbations in the horizontal velocity or the anisotropy parameter η. An iterative linearization of the eikonal equation is used as the basis for an algorithm of finite‐difference traveltime computations. A practical implementation of this iterative technique is to start with a background model that consists of an elliptically anisotropic, inhomogeneous medium, since traveltimes for this type of medium can be calculated efficiently using eikonal solvers, such as the fast marching method. This constrains the perturbation to changes in the anisotropy parameter η (the parameter most responsible for imaging improvements in anisotropic media). The iterative implementation includes repetitive calculation of η from traveltimes, which is then used to evaluate the perturbation needed for the next round of traveltime calculations using the linearized eikonal equation. Unlike isotropic media, interpolation is needed to estimate η in areas where the traveltime field is independent of η, such as areas where the wave propagates vertically.

Typically, two to three iterations can give sufficient accuracy in traveltimes for imaging applications. The cost of each iteration is slightly less than the cost of a typical eikonal solver. However, this method will ultimately provide traveltime solutions for VTI media. The main limitation of the method is that some smoothness of the medium is required for the iterative implementation to work, especially since we evaluate derivatives of the traveltime field as part of the iterative approach. If a single perturbation is sufficient for the traveltime calculation, which may be the case for weak anisotropy, no smoothness of the medium is necessary. Numerical tests demonstrate the robustness and efficiency of this approach.
Velocity analysis after migration
Authors: Silva Ron , Wang Yanghua
Published: March 2003

The double‐square‐root (DSR) equation used in pre‐stack migration is formulated in terms of velocity‐dependent and velocity‐independent terms. The velocity‐dependent term is shown to be the hyperbolic normal moveout (NMO) correction, whereas the velocity‐independent term is related to the recording geometry only. This separation of the velocity‐dependent term offers a means of applying vertical corrections to an initial migration velocity field. Using this concept, procedures are described both for velocity determination and for achieving improved structural imaging.

This decoupling is accurate both for constant‐velocity media and for media whose velocity varies as a function of depth. In media whose velocity varies as a function of both space and depth, a procedure is described for building velocity models through common‐image gather (CIG) stacking following prestack depth migration (PSDM) and time conversion (TC). This so‐called PSDM‐TC stack procedure provides a means of (a) incorporating both vertical and lateral velocity updates into an initial velocity model, (b) obtaining improved structural imaging by using a non‐optimal velocity model for the prestack depth migration, and (c) updating velocity by flattening CIGs and maximizing stack energy. The procedure can be applied to both P‐P wave and P‐SV wave migration.
Experimental soil warming effects on CO2 and CH4 flux from a low elevation spruce–fir forest soil in Maine, USA
Authors: RUSTAD LINDSEY E. , FERNANDEZ IVAN. J.
Published: March 2003

The effect of soil warming on CO2 and CH4 flux from a spruce–fir forest soil was evaluated at the Howland Integrated Forest Study site in Maine, USA from 1993 to 1995. Elevated soil temperatures (∼5 °C) were maintained during the snow‐free season (May – November) in replicated 15 × 15‐m plots using electric cables buried 1–2 cm below the soil surface; replicated unheated plots served as the control. CO2 evolution from the soil surface and soil air CO2 concentrations both showed clear seasonal trends and significant (P < 0.0001) positive exponential relationships with soil temperature. Soil warming caused a 25–40% increase in CO2 flux from the heated plots compared to the controls. No significant differences were observed between heated and control plot soil air CO2 concentrations which we attribute to rapid equilibration with the atmosphere in the O horizon and minimal treatment effects in the B horizon. Methane fluxes were highly variable and showed no consistent trends with treatment.
The influence of increasing growth temperature and CO2 concentration on the ratio of respiration to photosynthesis in soybean seedlings
Authors: ZISKA LEWIS H. , BUNCE JAMES A.
Published: March 2003

Using controlled environmental growth chambers, whole plants of soybean, cv. ‘Clark’, were examined during early development (7–20 days after sowing) at both ambient (≈ 350 μL L–1) and elevated (≈ 700 μL L–1) carbon dioxide and a range of air temperatures (20, 25, 30, and 35 °C) to determine if future climatic change (temperature or CO2 concentration) could alter the ratio of carbon lost by dark respiration to that gained via photosynthesis. Although whole‐plant respiration increased with short‐term increases in the measurement temperature, respiration acclimated to increasing growth temperature. Respiration, on a dry weight basis, was either unchanged or lower for the elevated CO2 grown plants, relative to ambient CO2 concentration, over the range of growth temperatures. Levels of both starch and sucrose increased with elevated CO2 concentration, but no interaction between CO2 and growth temperature was observed. Relative growth rate increased with elevated CO2 concentration up to a growth temperature of 35 °C. The ratio of respiration to photosynthesis rate over a 24‐h period during early development was not altered over the growth temperatures (20–35 °C) and was consistently less at the elevated relative to the ambient CO2 concentration. The current experiment does not support the proposition that global increases in carbon dioxide and temperature will increase the ratio of respiration to photosynthesis; rather, the data suggest that some plant species may continue to act as a sink for carbon even if carbon dioxide and temperature increase simultaneously.
Carbon accumulation, distribution and water use of Danthonia richardsonii swards in response to CO2 and nitrogen supply over four years of growth
Authors: LUTZE JASON L. , GIFFORD ROGER M.
Published: March 2003

Microcosms of Danthonia richardsonii (Cashmore) accumulated more carbon when grown under CO2 enrichment (719 μL L–1 cf. 359 μL L–1) over a four‐year period, even when nitrogen availability severely restricted productivity (enhancement ratios for total microcosm C accumulation of 1.21, 1.14 and 1.29 for mineral N supplies of 2.2, 6.7 and 19.8 g N m–2 y–1, respectively). The effect of CO2 enrichment on total system carbon content did not diminish with time. Increased carbon accumulation occurred despite the development over time of a lower leaf area index and less carbon in the green leaf fraction at high CO2. The extra carbon accumulated at high CO2 in the soil, senesced leaf and leaf litter fractions at all N levels, and in root at high‐N, while at low‐and mid‐N less carbon accumulated in the root fraction at high CO2. The rate of leaf turnover was increased under CO2 enrichment, as indicated by increases in the carbon mass ratio of senesced to green leaf lamina. Microcosm evapotranspiration rates were lower at high CO2 when water was in abundant supply, resulting in higher average soil water contents. The higher soil water contents at high CO2 have important implications for microcosm function, and may have contributed significantly to the increased carbon accumulation at high CO2. These results indicate that CO2 enrichment can increase carbon accumulation by a simple soil–plant system, and that any increase in whole system carbon accumulation may not be evident from snapshot measurements of live plant carbon.
Using an ecosystem model linked to GCM‐derived local weather scenarios to analyse effects of climate change and elevated CO2 on dry matter production and partitioning, and water use in temperate managed grasslands
Authors: Riedo Marcel , Gyalistras Dimitrios , Fischlin Andreas , Fuhrer JürG.
Published: March 2003

Local effects of climate change (CC) and elevated CO2 (2 × CO2, 660 μmol mol–1) on managed temperate grasslands were assessed by forcing a dynamic ecosystem model with weather scenarios. The aims of the study were to compare the relative importance of individual and combined effects of CC, 2 × CO2, and photosynthetic acclimation, and to assess the importance of local site conditions. The model was driven by hourly means for temperature (T), precipitation (P), global radiation (G), vapour pressure (VP), and wind speed (U). Local climate scenarios were derived by statistical downscaling techniques from a 2 × CO2 simulation with the General Circulation Model of the Canadian Climate Centre (CCC‐GCMII). Simulations over 14 growing seasons to account for year‐to‐year variability of climate were carried out for a low, relatively dry site, and a high, more humid site.

At both sites, shoot dry matter responded positively to 2 × CO2 with the site at low elevation being more sensitive than the higher site. The effect of assumed changes in climate was negative at the lower, but positive at the higher site. Shoot dry matter was more sensitive to the effects of 2 × CO2 than to CC. Both effects combined increased shoot dry matter by up to 20%. This was attributed to direct effects of 2 × CO2 and increased T, and indirect stimulation via increased soil N availability. Biomass partitioning to roots increased with 2 × CO2 but decreased with CC, while an intermediate response resulted from the combination. Leaf area index (LAI) increased under 2 × CO2, but not enough to compensate fully for a decrease in leaf conductance. Under the 2 × CO2 scenario evapotranspiration (ET) decreased, but increased under CC. Photosynthetic acclimation reduced the effect of 2 × CO2 on shoot growth, but had little effect on ET. The seasonal water use efficiency (WUE) was improved under 2 × CO2, and reduced under CC. With the combination of both factors, the change was small but still positive, especially at the high elevation site with more favourable soil water conditions. This reflects the stronger positive yield response in combination with a smaller increase in ET under cooler, more humid conditions.

The results for the combination of factors suggest that except for shoot growth, effects of 2 × CO2 and CC tend to offset each other. While CC determines the sign of the ET response, the sign of the biomass response is determined by 2 × CO2. The results highlight the importance of a site‐specific analysis of ecosystem responses by using a flexible approach based on a combination of state‐of‐the‐art downscaling, spatially resolved data sets, and a mechanistic model to obtain quantitative and reproducible assessments of climate change impacts at the ecosystem level.
A thirty percent increase in UV‐B has no impact on photosynthesis in well‐watered and droughted pea plants in the field
Authors: Allen D. J. , Nogués S. , Morison J. I. L. , Greenslade P. D. , Mcleod A. R. , Baker N. R.
Published: March 2003

It has been suggested that field experiments which increase UV‐B irradiation by a fixed amount irrespective of ambient light conditions (‘square‐wave’), may overestimate the response of photosynthesis to UV‐B irradiation. In this study, pea (Pisum sativum L.) plants were grown in the field and subjected to a modulated 30% increase in ambient UK summer UV‐B radiation (weighted with an erythemal action spectrum) and a mild drought treatment. UV‐A and ambient UV control treatments were also studied. There were no significant effects of the UV‐B treatment on the in situ CO2 assimilation rate throughout the day or on the light‐saturated steady‐state photosynthesis. This was confirmed by an absence of UV‐B effects on the major components contributing to CO2 assimilation; photosystem II electron transport, ribulose 1,5‐bisphosphate regeneration, ribulose 1,5‐bisphosphate carboxylase/oxygenase carboxylation, and stomatal conductance. In addition to the absence of an effect on photosynthetic activities, UV‐B had no significant impact on plant biomass, leaf area or partitioning. UV‐B exposure increased leaf flavonoid content. The UV‐A treatment had no observable effect on photosynthesis or productivity. Mild drought resulted in reduced biomass, a change in partitioning away from shoots to roots whilst maintaining leaf area, but had no observable effect on photosynthetic competence. No UV‐B and drought treatment interactions were observed on photosynthesis or plant biomass. In conclusion, a 30% increase in UV‐B had no effects on photosynthetic performance or productivity in well‐watered or droughted pea plants in the field.
Impulse response functions of terrestrial carbon cycle models: method and application
Authors: Thompson Matthew V. , Randerson James T.
Published: March 2003

To provide a common currency for model comparison, validation and manipulation, we suggest and describe the use of impulse response functions, a concept well‐developed in other fields, but only partially developed for use in terrestrial carbon cycle modelling. In this paper, we describe the derivation of impulse response functions, and then examine (i) the dynamics of a simple five‐box biosphere carbon model; (ii) the dynamics of the CASA biosphere model, a spatially explicit NPP and soil carbon biogeochemistry model; and (iii) various diagnostics of the two models, including the latitudinal distribution of mean age, mean residence time and turnover time. We also (i) deconvolve the past history of terrestrial NPP from an estimate of past carbon sequestration using a derived impulse response function to test the performance of impulse response functions during periods of historical climate change; (ii) convolve impulse response functions from both the simple five‐box model and the CASA model against a historical record of atmospheric δ13C to estimate the size of the terrestrial 13C isotopic disequilibrium; and (iii) convolve the same impulse response functions against a historical record of atmospheric 14C to estimate the 14C content and isotopic disequilibrium of the terrestrial biosphere at the 1° × 1° scale. Given their utility in model comparison, and the fact that they facilitate a number of numerical calculations that are difficult to perform with the complex carbon turnover models from which they are derived, we strongly urge the inclusion of impulse response functions as a diagnostic of the perturbation response of terrestrial carbon cycle models.
Emissions of carbon from forestry and land‐use change in tropical Asia
Authors: Houghton R. A. , Hackler J. L.
Published: March 2003

The net emissions of carbon from forestry and changes in land use in south and southeast Asia were calculated here with a book‐keeping model that used rates of land‐use change and associated per hectare changes in vegetation and soil to calculate changes in the amount of carbon held in terrestrial ecosystems and wood products. The total release of carbon to the atmosphere over the period 1850–1995 was 43.5 PgC. The clearing of forests for permanent croplands released 33.5 PgC, about 75% of the total. The reduction of biomass in the remaining forests, as a result of shifting cultivation, logging, fuelwood extraction, and associated regrowth, was responsible for a net loss of 11.5 PgC, and the establishment of plantations withdrew from the atmosphere 1.5 PgC, most of it since 1980. Based on comparisons with other estimates, the uncertainty of this long‐term flux is estimated to be within ±30%. Reducing this uncertainty will be difficult because of the difficulty of documenting the biomass of forests in existence >40 years ago. For the 15‐y period 1981–1995, annual emissions averaged 1.07 PgC y–1, about 50% higher than reported for the 1980s in an earlier study. The uncertainty of recent emissions is probably within ± 50% but could be reduced significantly with systematic use of satellite data on changes in forest area. In tropical Asia, the emissions of carbon from land‐use change in the 1980s accounted for approximately 75% of the region’s total carbon emissions. Since 1990 rates of deforestation and their associated emissions have declined, while emissions of carbon from combustion of fossil fuels have increased. The net effect has been a reduction in emissions of CO2 from this region since 1990.
Effects of elevated ultraviolet radiation on Quercus robur and its insect and ectomycorrhizal associates
Authors: Newsham K. K. , Greenslade P. D. , Mcleod A. R.
Published: March 2003

Saplings of pedunculate oak (Quercus robur L.) were exposed at an outdoor facility to modulated levels of elevated UV‐B radiation (280–315 nm) under treatment arrays of cellulose diacetate‐filtered fluorescent lamps which also produced UV‐A radiation (315–400 nm). Saplings were also exposed to UV‐A radiation alone under control arrays of polyester‐filtered lamps and to ambient levels of solar radiation under arrays of unenergized lamps. The UV‐B treatment corresponded to a 30% elevation above the ambient level of erythemally weighted UV‐B radiation. Sapling growth and the occurrence of associated organisms were examined over two years. In both years, leaves of saplings exposed to UV‐B treatment were thicker and smaller in area relative to leaves exposed to ambient and control levels of radiation. UV‐B treatment also retarded bud burst at one sampling in the first year of the study. Some responses were recorded which were common to both treatment and control arrays, implying that UV‐A radiation, or some other factor associated with energized lamps, was responsible for the observed effects. Saplings under treatment and control arrays were taller in the first year of the study, suffered greater herbivory from chewing insects, and had lower root dry weights and greater insertion heights of secondary branches than saplings exposed to ambient levels of radiation. Exposure of saplings to elevated UV‐A radiation alone under control arrays increased estimated leaf volumes in the second year of the study and reduced the number of secondary branches and the total number of branches per sapling after two years, relative to both treatment and ambient arrays. There were no effects of elevated ultraviolet radiation on shoot or total plant weight, root/shoot ratios, stem diameter, the numbers or insertion heights of primary or tertiary branches, total leaf number, timing of leaf fall or frequency of ectomycorrhizas. Our study suggests that any increases in UV‐B radiation as a result of stratospheric ozone depletion will influence the growth of Q. robur primarily through effects on leaf morphology.
Responses of stomatal conductance to light, humidity and temperature in winter wheat and barley grown at three concentrations of carbon dioxide in the field
Authors: Bunce James A.
Published: March 2003

Responses of leaf stomatal conductance to light, humidity and temperature were characterized for winter wheat and barely grown at ambient (about 350 μmol mol−1 in the daytime), ambient + 175 and ambient + 350 μmol mol−1 concentrations of carbon dioxide in open‐topped chambers in field plots over a three year period. Stomatal responses to environment were determined by direct manipulation of single environmental factors, and those results were compared with responses derived from natural day to day variation in mid‐day stomatal conductance. The purpose of these experiments was to determine the magnitude of reduction in stomatal conductance at elevated [CO2], and to assess whether the relative response of conductance to elevated [CO2] was constant across light, humidity and temperature conditions. The results indicated that light, humidity and temperature all significantly affected the relative decrease in stomatal conductance at elevated [CO2]. The relative decrease in conductance with elevated [CO2] was greater at low light, low water vapour pressure difference, and high temperature in both species. For measurements made at saturating light near mid‐day, the ratio of mid‐day stomatal conductances at doubled [CO2] to that at ambient [CO2] ranged from 0.42 to 0.86, with a mean of 0.66 in barley, and from 0.33 to 0.80, with a mean of 0.56 in wheat. Day‐to‐day variation in the relative effect of elevated [CO2] on conductance was correlated with the relative stimulation of [CO2] assimilation rate and with temperature. Some limitations of multiple linear regression, multiplicative, and ‘Ball–Berry' models as summaries of the data are discussed. In barley, a better fit to the models occurred in individual years than for the combined data, and in wheat a better fit to the models occurred when data from near the end of the season were removed.