bluuebunny/crossref_metadata_2025 huggingface dataset:
Hierarchical and co‐operative binding of OmpR to a fusion construct containing the ompC and ompF upstream regulatory sequences of Escherichia coli
Authors: Bergstrom Lisa C. , Qin Ling , Harlocker Susan L. , Egger Linda A. , Inouye Masayori
Published: March 2003

Background: OmpR is a transcription factor that regulates the expression of the porin genes ompF and ompC in Escherichia coli. The phosphorylation state of OmpR, directed by the osmosensor EnvZ, determines its ability to bind to the upstream regulatory regions of these genes, a total of 14 phospho‐OmpR binding sites. While it has been possible to study the stoichiometry and hierarchy of the OmpR–DNA interaction in the upstream regions of ompF and ompC, their disunited location on the bacterial chromosome has made it difficult to compare the individual binding affinities of respective sites.

Results: Using 1,10‐phenanthroline‐Cu+ footprinting on a fused construct containing both the ompF and ompC upstream regulatory sequences, and gel shift experiments on oligomers corresponding to individual sites, we have established a comparative hierarchy for OmpR binding, as F1, C1 > F2, F3 > C2 > C3. In addition, the binding patterns reveal an apparent co‐operative relationship between OmpR molecules bound at several upstream motifs. Densitometric analyses of the footprinted regions provide support for these observations. Mutational analysis of this construct reveals that the alteration of a conserved cytidine in the F1 motif (–86) causes a loss of OmpR affinity and disrupts hierarchical OmpR‐binding in the entire ompF region.

Conclusions: The present results provide a unique view of the OmpR interaction with the two respective promoters, ompF and ompC, and an insight into the question of how the expression of ompF and ompC are reciprocally regulated by medium osmolarity.
Transmembrane tyrosine phosphatase LAR induces apoptosis by dephosphorylating and destabilizing p130Cas
Authors: Weng Liang‐Ping , Wang Xin , Yu Qiang
Published: March 2003

Background:

LAR is a transmembrane receptor‐like protein tyrosine phosphatase (PTP). Genetic studies of Drosophila LAR suggest that LAR may function to regulate cell adhesions or adhesion‐mediated signal transduction. The over‐expression of LAR in mammalian tissue culture cells does not affect cell adhesion but induces caspase‐dependent apoptosis. This study investigates molecular mechanisms of LAR‐induced apoptosis by searching for in vivo substrates of LAR which are responsible for LAR‐induced apoptosis.

Results:

The over‐expression of LAR in tissue culture cells specifically decreased the steady state protein level of p130Cas, a multifunctional signal assembly protein in signal transduction, by reducing the tyrosine phosphorylation and protein stability of p130Cas. The reduction of p130Cas protein level could be inhibited by tyrosine phosphatase inhibitors. Phosphatase domain‐deleted mutant LARs had no effect on p130Cas. LAR also preferentially dephosphorylated p130Casin vitro. Subcellularly, LAR and p130Cas were co‐localized along stress fibres and at focal adhesions. LAR over‐expression eliminated p130Cas from focal adhesions without affecting focal adhesion assembly. Restoring the level of p130Cas alleviated LAR‐induced apoptosis.

Conclusions:

p130Cas is an in vivo substrate of LAR. LAR specifically dephosphorylates and destabilizes p130Cas and may play a role in regulating cell adhesion‐mediated cell survival. The function of p130Cas in focal adhesions may not be to regulate focal adhesion assembly and cell adhesion but rather to transduce the cell adhesion‐generated signals which are essential for cell survival.
High copy number suppression of the meiotic arrest caused by a dmc1 mutation: REC114 imposes an early recombination block and RAD54 promotes a DMC1‐independent DSB repair pathway
Authors: Bishop Douglas K. , Nikolski Yuri , Oshiro June , Chon Jason , Shinohara Miki , Chen Xi
Published: March 2003

Background

DMC1, the meiosis‐specific eukaryotic homologue of bacterial recA, is required for completion of meiotic recombination and cell cycle progression past prophase. In a dmc1 mutant, double strand break recombination intermediates accumulate and cells arrest in prophase. We isolated genes which, when present at high copy numbers, suppress the meiotic arrest phenotype conferred by dmc1 mutations.

Results

Among the genes isolated were two which suppress arrest by altering the recombination process. REC114 suppresses formation of double strand break (DSB) recombination intermediates. The low viability of spores produced by dmc1 mutants carrying high copy numbers of REC114 is rescued when reductional segregation is bypassed by mutation of spo13. High copy numbers of RAD54 suppress dmc1 arrest, promote DSB repair, and allow formation of viable spores following reductional segregation. Analysis of the combined effects of a null mutation in RED1, a gene required for meiotic chromosome structure, with null mutations in RAD54 and DMC1 shows that RAD54, while not normally important for repair of DSBs during meiosis, is required for efficient repair of breaks by the intersister recombination pathway that operates in red1 dmc1 double mutants.

Conclusions

Over‐expression of REC114 suppresses meiotic arrest by preventing formation of DSBs. High copy numbers of RAD54 activate a DMC1‐independent mechanism that promotes repair of DSBs by homology‐mediated recombination. The ability of RAD54 to promote DMC1‐independent recombination is proposed to involve suppression of a constraint that normally promotes recombination between homologous chromatids rather than sisters.
Control of genetic stability in Escherichia coli: the SbcB 3′‐5′ exonuclease suppresses illegitimate recombination promoted by the RecE 5′‐3′ exonuclease
Authors: Yamaguchi Hirotaka , Hanada Katsuhiro , Asami Yasuo , Kato Jun‐ichi , Ikeda Hideo
Published: March 2003

Background

The EscherichiacolisbcB gene, which codes for a 3′‐5′ exonuclease, ExoI, is known to suppress illegitimate recombination. In contrast, the recE gene, which codes for a 5′‐3′ exonuclease, Exo VIII promotes joining between DNA ends having short stretches of homology. Therefore, it seems likely that the 3′‐5′ and 5′‐3′ exonucleases regulate genetic instability that is mediated by illegitimate recombination. However, there has been little evidence to substantiate the involvement of exonuclease activity in the promotion and suppression of illegitimate recombination.

Results

Using a plasmid system for the analysis of deletion formation, we first demonstrated that deletion formation is increased by the sbcA mutation, which activates the expression of RecE 5′‐3′ exonuclease. It is thought that DNA ends having 3′‐single stranded overhangs are important for illegitimate recombination. Next, we found that a large supply of SbcB 3′‐5′ exonuclease suppresses the deletion formation enhanced by the RecE exonuclease. Moreover, the SbcB exonuclease even suppressed deletion formation in cells not expressing RecE exonuclease.

Conclusion

We conclude that DNA ends with 3′‐overhangs produced by 5′‐3′ dsDNA exonuclease activity are proficient for illegitimate recombination, while blunt DNA ends produced by 3′‐5′ ssDNA exonuclease activity are deficient for illegitimate recombination. Therefore, both exonucleases may play important roles in genetic stability by controlling end‐joining between DNA molecules.
Importance of spatial activation of Cdc42 and Rac small G proteins by frabin for microspike formation in MDCK cells
Authors: Yasuda Takeo , Ohtsuka Toshihisa , Inoue Eiji , Yokoyama Shigekazu , Sakisaka Toshiaki , Kodama Atsuko , Takaishi Kenji , Takai Yoshimi
Published: March 2003

Background

Frabin is an actin filament (F‐actin)‐binding protein that shows GDP/GTP exchange activity for Cdc42 small G protein (Cdc42). Frabin furthermore induces indirect activation of Rac small G protein (Rac) in intact cells. We have recently shown that in nonepithelial cells, frabin induces the formation of both filopodia‐ and lamellipodia‐like processes through the activation of Cdc42 and Rac, respectively. In epithelial cells such as MDCK cells, Cdc42 and Rac regulate cell‐cell adherens junctions (AJs) via the accumulation of F‐actin and E‐cadherin, although neither Cdc42 nor Rac induces the formation of filopodia or lamellipodia. In this study, we have examined the effects of frabin on the reorganization of the actin cytoskeleton in MDCK cells.

Results

Frabin induces the formation of microspikes at the basal area of the lateral membranes through the activation of Cdc42 and Rac in MDCK cells, although a dominant active mutant of Cdc42 or Rac alone, or both, did not induce the formation of microspikes. Furthermore, frabin weakly increased the accumulation of F‐actin and E‐cadherin at cell‐cell AJs and the formation of stress fibres through the activation of Cdc42 and Rac, under conditions where the dominant active mutant of Cdc42 or Rac markedly showed these effects. The Cdc42‐ and Rac‐induced formation of stress fibres was dependent on the activation of Rho small G protein.

Conclusion

These results indicate that the frabin‐dependent spatial activation of Cdc42 and Rac is important for the formation of microspikes.
The role of tightly bound ATP in Escherichia coli tRNA nucleotidyltransferase
Authors: Tomari Yukihide , Suzuki Tsutomu , Watanabe Kimitsuna , Ueda Takuya
Published: March 2003

Background

The CCA‐adding enzyme [ATP(CTP): tRNA nucleotidyltransferase (EC. 2.7.7.25)] catalyses the addition of the conserved CCA sequence to the 3′‐terminus of tRNAs. All CCA‐adding enzymes are classified into the nucleotidyltransferase superfamily. In the absence of ATP, the Escherichia coli CCA‐adding enzyme displays anomalous poly(C) polymerase activity.

Results

We show that CCA‐adding enzyme over‐expressed in E. coli exists in an ATP‐bound form. The affinities of ATP and CTP towards the enzyme were estimated by several methods, and the dissociation constants for ATP and CTP were determined to be 6.3 and 188 μm, respectively. AMP‐incorporation terminated the nucleotidyltransferase reaction, while in the absence of ATP, the enzyme continued poly(C) polymerization. In the case of a tRNA substrate with a mutation in the T‐loop region, normal CC was added at a much slower rate compared with the wild‐type, but anomalous poly(C) polymerization occurred at the same rate as in the wild‐type.

Conclusion

Based on the findings outlined above, we concluded that the E. coli CCA‐adding enzyme possesses at least two distinct nucleotide binding sites, one responsible for ATP binding and the other(s) for CTP binding. The addition of ATP from the tight ATP binding site terminates nucleotide incorporation, thus limiting poly(C) polymerization to CCA. It is also suggested that during anomalous poly(C) polymerization, tRNA translocates from the tRNA binding site upon the third C addition.
Expression of herpes simplex virus type 2 US3 affects the Cdc42/Rac pathway and attenuates c‐Jun N‐terminal kinase activation
Authors: Murata Takayuki , Goshima Fumi , Daikoku Tohru , Takakuwa Hiroki , Nishiyama Yukihiro
Published: March 2003

Although the US3 gene product of herpes simplex virus (HSV) has been identified as a serine/threonine protein kinase (PK), the functions are poorly understood.

We found that US3 PK of HSV‐2 induced disruption of actin filaments, cell rounding and accumulation of binucleate cells in HEp2 cells. Cell rounding was abrogated by expression of either kinase‐dead forms of US3 PK or a mutant protein lacking the acidic cluster in the kinase regulatory domain. Co‐expression of dominant active forms of Cdc42/Rac inhibited cell rounding, suggesting that a signal transduction pathway involving Cdc42/Rac may play a role in the morphological changes induced by the kinase. Cdc42 and Rac, members of the Rho family of small GTPases, function as molecular switches changing actin cytoskeletal organization, influencing transcription and controlling apoptotic cell death. By computed homology search, we noticed significant similarities between US3 PK and p21‐activated kinase (PAK), which is activated by the Cdc42 or Rac. We also found that the expression of US3 suppressed the activation of c‐Jun N‐terminal kinase (JNK), a kinase that is downstream of PAK.

These observations suggest that the US3 PK affects the Cdc42/Rac pathway and can act as an upstream suppressor of JNK in the stress‐activated signalling pathway.
Regulation of gene expression, cellular localization, and in vivo function of Caenorhabditis elegans DNA topoisomerase I
Authors: Lee Myon Hee , Park Hyungki , Shim Gaegal , Lee Junho , Koo Hyeon‐Sook
Published: March 2003

Background

DNA topoisomerase I is dispensable in yeast, but is essential during the embryogenesis of Drosophila and mouse. In order to determine functions of the enzyme in the development of Caenorhabditis elegans, phenotypes resulting from the deficiency were observed and correlated with the expression of the gene.

Results

The transcriptional regulation of the C. elegans DNA topoisomerase I gene was investigated by mRNA localization and reporter gene expression in C. elegans. The mRNA was expressed in the gonad and in the early embryos, followed by a rapid decrease in its level during the late embryonic stage. A reporter gene expression induced by the 5′‐upstream DNA sequence appeared at the comma stage of embryos, continued through the L1 larval stage, and began to decrease gradually afterwards. The DNA topoisomerase I protein was immuno‐localized in the nuclei of meiotic gonad cells and interphase embryonic cells, and unexpectedly in centrosomes of mitotic embryonic cells. Double‐stranded RNA interference of DNA topoisomerase I gene expression resulted in pleiotropic phenotypes showing abnormal gonadogenesis, oocyte development and embryogenesis.

Conclusion

These phenotypes, along with expressional regulations, demonstrate that DNA topoisomerase I plays important roles in rapidly growing germ cells and embryonic cells.
Arabidopsis transcriptional regulation by light stress via hydrogen peroxide‐dependent and ‐independent pathways
Authors: Kimura Mitsuhiro , Yoshizumi Takeshi , Manabe Katsushi , Yamamoto Yoshiharu Y. , Matsui Minami
Published: March 2003

Background High (intense) light stress causes the formation of oxygen radicals in chloroplasts and has the potential to damage them. However, plants are able to respond to this stress and protect the chloroplasts by various means, including transcriptional regulation in the nucleus. Although the corresponding signalling pathway is largely unknown, the high light response in the expression of the Arabidopsis APX2 gene is reported to be mediated by hydrogen peroxide.

Results We characterized light stress signalling by analysing expression profiles of another high light‐inducible gene of Arabidopsis, ELIP2, with the aid of an ELIP2 promoter‐luciferase gene fusion. The established ELIP2::LUC transgenic Arabidopsis showed activation by high light, but not by hydrogen peroxide. On the other hand, the native ELIP2 gene as well as the APX2 gene was activated by the hydrogen peroxide. The activation of ELIP2::LUC by intense light was not inhibited by K252a but by okadaic acid.

Conclusion The light stress signalling from the chloroplast to the nucleus is revealed to be mediated through at least two pathways: both hydrogen peroxide‐dependent and –independent. The latter pathway is thought to be mediated by the protein phosphatase 2A/1 activity that is suppressed by okadaic acid.
Bir1/Cut17 moving from chromosome to spindle upon the loss of cohesion is required for condensation, spindle elongation and repair
Authors: Morishita Jun , Matsusaka Takahiro , Goshima Gohta , Nakamura Takahiro , Tatebe Hisashi , Yanagida Mitsuhiro
Published: March 2003

Background In mammals, proteins containing BIR domains (IAPs and survivin) are implicated in inhibiting apoptosis and sister chromatid separation. In the nematode, Bir1 is required for a proper localization of aurora kinase, which moves from the mitotic chromosome in metaphase to the spindle midzone in anaphase as a passenger. Fission yeast Bir1/Pbh1 is essential for normal mitosis.

Results A temperature sensitive mutant cut17‐275 exhibits the defect in condensation and spindle elongation at 36 °C, while securin is degraded. Gene cloning shows that the cut17+ gene is identical to bir1+/pbh1+. At 26 °C, cut17‐275 is UV sensitive as the repair of DNA damage is severely compromised. Bir1/Cut17 is a nuclear protein in interphase, which is then required for recruiting condensin to the mitotic nucleus, and concentrates to form a discrete number of dots from prometaphase to metaphase. Once the chromatids are separated, Bir1/Cut17 no longer binds to kinetochores and instead moves to the middle of spindle. Chromatin immunoprecipitation suggested that Bir1/Cut17 associates with the outer repetitious centromere region in metaphase. Following the initiation of anaphase the protein switches from being a chromosomal protein to a spindle protein. This transit is stringently regulated by the state of sister chromatid cohesion proteins Mis4 and Rad21. Ark1, is an aurora kinase homologue whose mitotic distribution is identical to, and under the control of Bir1/Cut17.

Conclusions Bir1/Cut17 and Ark1 act as ‘passengers’ but they may play a main role as a recruitment factor, essential for condensation, spindle elongation and DNA repair. Bir1/Cut17 should have roles both in mitotic and in interphase chromosome. The proper location of Ark1 requires Bir1/Cut17, and the mitotic localization of Bir1/Cut17 requires sister cohesion.
Regulation of the activity of the transcription factor Runx2 by two homeobox proteins, Msx2 and Dlx5
Authors: Shirakabe Kyoko , Terasawa Kazuya , Miyama Katsuyoshi , Shibuya Hiroshi , Nishida Eisuke
Published: March 2003

Background Runx2, formerly called PEBP2αA or Cbfa1, is a transcription factor whose deletion causes a complete lack of ossification. It directly regulates the expression of osteoblast‐specific genes through the osteoblast‐specific cis‐acting element found in the promoter region of these genes.

Results In this study, we have found conditions in which induction of the expression of Runx2 is not accompanied by expression of an osteoblast‐specific gene, osteocalcin in C2C12 cells. This finding suggests the existence of a repressor of the activity of Runx2. We have then found that the homeobox protein Msx2 is able to repress the transcription activity of Runx2 by interacting with it. Furthermore, our results have shown that the other homeobox protein Dlx5 has an activity which interferes with both abilities of Msx2 to interact with Runx2 and repress its transcription activity. It has previously been shown that a missense mutation of Msx2 (P148H) causes Boston‐type craniosynostosis in humans. Interestingly, while this mutant form of Msx2 was able to bind to Runx2 and repress its activity, these abilities of Msx2 (P148H) were not subject to regulation by Dlx5.

Conclusion These results suggest that regulation of the activity of Runx2 by Msx2 and Dlx5 plays an important role in the mammalian skull development.
ICRF‐193, a catalytic inhibitor of DNA topoisomerase II, inhibits re‐entry into the cell division cycle from quiescent state in mammalian cells
Authors: Hossain Muktadir S. , Akimitsu Nobuyoshi , Takaki Tohru , Hirai Hiroshi , Sekimizu Kazuhisa
Published: March 2003

Background: To describe the requirement of DNA topoisomerase II (topo II) during transition from the quiescent state (G0 phase) to the cell division cycle in mammalian cells, we examined the influence of ICRF‐193, a catalytic inhibitor of topo II, on re‐entry into the cell division cycle of quiescent cells in response to appropriate growth stimuli.

Results: The re‐entry into the S phase of cultured cell lines arrested at the quiescent (G0) phase by serum‐starvation was sensitive to 10 µm ICRF‐193. DNA syntheses induced by lipopolysaccharide in murine spleen cells or by release from contact‐inhibition were also inhibited by ICRF‐193. The cell lines with a high‐level of resistance toward ICRF‐193 due to a point mutation in the topo IIα gene entered into the S phase from quiescence in the presence of ICRF‐193. The drug did not inhibit entry into the S phase in cultured cells released from arrest at the metaphase or G1 phase.

Conclusion: There is an ICRF‐193‐sensitive step during re‐entry of quiescent mammalian cells into the cell division cycle upon growth stimulation and the drug targets topo IIα during the process.
Genome‐wide analysis of changes in early gene expression induced by oestrogen
Authors: Watanabe Hajime , Suzuki Atsuko , Mizutani Takeshi , Khono Satomi , Lubahn Dennis B. , Handa Hiroshi , Iguchi Taisen
Published: March 2003

Background: The sex hormone 17β‐oestradiol (E2) has profound effects on many aspects of reproduction, development, as well as behaviour. Although the oestrogen receptor is well characterized on a molecular level, relatively few genes affected by E2 have been identified, and the mechanisms underlying the physiological changes caused by E2 are largely unknown. In order to identify oestrogen‐regulated genes in vivo, early uterine gene expression profiles were developed using DNA microarrays.

Results: Ovariectomized mice were exposed to 17β‐oestradiol for 6 h, and mRNA expression analysis for 9977 genes was performed. Although a large number of genes was affected by oestrogen administration, the genes that showed higher reproducibility in repetitive experiments were selected and further examined. For most of the selected genes, expression was induced in a dose‐dependent manner, and gene expression was not altered following oestrogen treatment in oestrogen receptor‐α (ERα)‐deficient mice. In combination with the estimation of gene expression levels using quantitative PCR, it was revealed that multiple genes related to sterol biosynthesis, tRNA synthesis, RNA processing, and growth signalling were activated. Based on the microarray data, we selected additional genes related to sterol biosynthesis and tRNA synthesis and confirmed that these genes are also activated by oestrogen.

Conclusion: Genes suggesting a basis for the drastic uterotrophic effect observed several days following oestrogen administration were identified. These findings not only reveal the diverse effect of oestrogen signalling on transcript levels in vivo but also demonstrate the ability of DNA microarrays to identify cellular pathways affected by oestrogen.
MCM3‐binding GANP DNA‐primase is associated with a novel phosphatase component G5PR
Authors: Kono Yoshihiko , Maeda Kazuhiko , Kuwahara Kazuhiko , Yamamoto Hideyuki , Miyamoto Eishichi , Yonezawa Kazuyoshi , Takagi Katsumasa , Sakaguchi Nobuo
Published: March 2003

Background: GANP, carrying DNA‐primase and MCM3‐binding domains, is up‐regulated in germinal centre B cells. To understand the regulatory function of GANP upon MCM complex, we searched for GANP‐associated molecules by yeast two‐hybrid screening.

Results: Using the 1 kb fragment (G5) of the ganp cDNA, we identified a clone named G5PR that is structurally homologous to known regulatory subunits of protein phosphatases (PPases) and determined the association of G5PR with GANP in vivo in the DNA transfectant. G5PR is associated with protein phosphatase 5 (PP5) through its tetratricopeptide‐repeat (TPR) domain. Pull‐down assays demonstrated that G5PR is also associated with protein phosphatase 2A (PP2A), the complex of A subunit (PR65) and the catalytic (C) subunit (PP2Ac), similar to the B′′ subunit. The G5PR‐associated complex had phosphatase activity on casein, histone H1 and MCM3 in vitro, but the addition of G5PR did not stimulate or inhibit the phosphatase activities of PP5 and PP2A. The cellular localization of G5PR in transfected cells varies during cell cycling, appearing in the nucleus during prophase, in the peri‐chromatin during mitotic phase, and in the cytoplasm after cell division.

Conclusion: G5PR is capable of recruiting two kinds of PPases, PP5 and PP2A, into the GANP/MCM3 complex, which might regulate its phosphorylation state during cell cycle progression.
An algebraic formulation of geophysical inverse problems
Authors: Vasco D. W.
Published: March 2003

Many geophysical inverse problems derive from governing partial differential equations with unknown coefficients. Alternatively, inverse problems often arise from integral equations associated with a Green's function solution to a governing differential equation. In their discrete form such equations reduce to systems of polynomial equations, known as algebraic equations. Using techniques from computational algebra one can address questions of the existence of solutions to such equations as well as the uniqueness of the solutions. The techniques are enumerative and exhaustive, requiring a finite number of computer operations. For example, calculating a bound to the total number of solutions reduces to computing the dimension of a linear vector space. The solution set itself may be constructed through the solution of an eigenvalue problem. The techniques are applied to a set of synthetic magnetotelluric values generated by conductivity variations within a layer. We find that the estimation of the conductivity and the electric field in the subsurface, based upon single-frequency magnetotelluric field values, is equivalent to a linear inverse problem. The techniques are also illustrated by an application to a magnetotelluric data set gathered at Battle Mountain, Nevada. Surface observations of the electric (E  y) and magnetic (H  x) fields are used to construct a model of subsurface electrical structure. Using techniques for algebraic equations it is shown that solutions exist, and that the set of solutions is finite. The total number of solutions is bounded above at 134 217 728. A numerical solution of the algebraic equations generates a conductivity structure in accordance with the current geological model for the area.
Analysis and application of a non‐conventional underwater geoelectrical method in Lake Geneva, Switzerland
Authors: Baumgartner François , Christensen Niels B.
Published: March 2003

The electrical method presented is used for determining the resistivity of lake‐bottom sediments and is based on the d.c. electrical sounding principles. The electrode array, called the fishing rod (FR), is of pole‐pole type and is orientated vertically on a line perpendicular to the surface of the water. The technique is used for mapping resistivity anomalies located deep underwater. This paper presents an analysis of the resolution capabilities of the FR method and the results of a case study carried out in Lake Geneva, where measurements were interpreted using a one‐dimensional (1D) multilayer earth model. The analysis of the uncertainty in the model parameters of a 1D multilayer earth model is carried out using the covariance matrix of the linearized inversion problem. The results of the analyses show that when the thickness and resistivity of the water layer is known, the resistivity of the sediment layer is well determined under most circumstances. The thickness of the sediment layer is well determined when resistivity contrasts are not too low. In Lake Geneva the FR method has been used to study an old depression with a resistive channel. This application shows the efficiency of the method compared with conventional electrical methods, where water depth becomes a limiting factor. The use of an automated iterative inversion scheme in this particular case is advantageous, as a joint interpretation of the three different data sets measured with the FR method can be carried out. Finally, the result of the inversion is compared with the trial‐and‐error interpretations of a previous study.
Short note: A simple nomogram for interpretation due to magnetic horizontal cylinders
Authors: Kara Ibrahim , Aydogan Davut , Ahmet Yüksel F.
Published: March 2003

The magnetic anomaly ΔF due to a long horizontal cylinder yields three points related to its extrema. A nomogram is presented for the determination of some source parameters of the causative body.
A shear experiment over the Natih field in Oman: pilot seismic and borehole data
Authors: Hake J.H. , Gevers E.C.A. , Van Der Kolk C.M. , Tichelaar B.W.
Published: March 2003

An experimental multicomponent three‐dimensional (3D) seismic survey has been carried out over the Natih field in Oman. This paper describes the small‐scale two‐dimensional experiment carried out beforehand, and how the results obtained from this pilot were used to assess the feasibility of a nine‐component three‐dimensional (9C3D) operation as well as to determine the field parameters for the field‐scale 3D survey. It also describes the two VSPs and a wireline shear log, acquired in conjunction with the pilot experiment, and the importance of such borehole data for establishing the correct time‐to‐depth relationship for the seismic data and for providing an independent check on the seismic interpretation. The observation of cusps in the offset VSP indicated the strong anisotropy of the Fiqa shales overlying the Natih reservoir.
Comparison of six different methods for calculating traveltimes
Authors: Leidenfrost  , Ettrich  , Gajewski  , Kosloff
Published: March 2003

We study six different methods for the calculation of seismic traveltimes. All methods yield traveltimes at all points of a regular grid.

The methods examined comprise three different variants of finite‐difference (FD) eikonal solvers, the graph method, wavefront construction and a combined FD and Runge–Kutta method.

The main points of investigation are computational time, accuracy and memory requirements. We took measures to obtain a high level of both general validity and clear understanding of the results. We used a profiling program to be able to measure the time that the actual core algorithm needs, thus avoiding any overhead of highly system‐dependent in‐/output operations.

The comparison shows that no single method is the most appropriate but that the choice depends on the task to be fulfilled. The FD eikonal solver that uses expanding squares proves to be best suited for models which are not too complicated because it offers the best compromise between speed and accuracy, whereas wavefront construction should be applied to complex media because of its superior reliability which then justifies the much higher computational times.
Combining two seismic experiments to attenuate free‐surface multiples in OBC data*
Authors: Ikelle Luc T.
Published: March 2003

The current inverse scattering solution used for multiple attenuation of marine seismic reflection data assumes that sources and receivers are located in the water. To adapt this solution to the ocean‐bottom cable (OBC) experiment where receivers are located on the sea‐floor, we have proposed combining the conventional marine surface seismic reflection data (streamer data) with OBC data. The streamer data add to the OBC data some of the wave paths needed for multiple attenuation. This combination has allowed us to develop a multiple attenuation method for OBC data which does not require any knowledge of the subsurface and which takes into account all free‐surface multiples, including receiver ghosts. A non‐linear synthetic data example consisting of pressure and particle velocity fields is used to illustrate the procedure.
Crooked line, rough topography: advancing towards the correct seismic image
Authors: Gray Samuel H. , Maclean Gary , Marfurt Kurt J.
Published: March 2003

Seismic exploration in mountainous areas imposes serious compromises on both acquisition and processing. Access restrictions usually result in profiles that are not straight and are not recorded along the true dip direction (if there is a true dip direction!). Processing constraints often result in very poor approximate corrections for elevations and for deviations from a straight line. Most fundamentally, 2D acquisition and processing assumes that the earth is 2D; this assumption is often seriously violated in mountainous areas. While we cannot efficiently correct 2D seismic data for the effects of a fully 3D subsurface, we can improve the data quality in thrust areas where the assumption of 2D subsurface variation is reasonable. We do this in a series of small steps, which improves the accuracy of several approximations made in processing 2D land data.
An electromagnetic modelling tool for the detection of hydrocarbons in the subsoil
Authors: Carcione  , Seriani
Published: March 2003

Electromagnetic geophysical methods, such as ground‐penetrating radar (GPR), have proved to be optimal tools for detecting and mapping near‐surface contaminants. GPR has the capability of mapping the location of hydrocarbon pools on the basis of contrasts in the effective permittivity and conductivity of the subsoil. At radar frequencies (50 MHz to 1 GHz), hydrocarbons have a relative permittivity ranging from 2 to 30, compared with a permittivity for water of 80. Moreover, their conductivity ranges from zero to 10 mS/m, against values of 200 mS/m and more for salt water. These differences indicate that water/hydrocarbon interfaces in a porous medium are electromagnetically ‘visible’. In order to quantify the hydrocarbon saturation we developed a model for the electromagnetic properties of a subsoil composed of sand and clay/silt, and partially saturated with air, water and hydrocarbon. A self‐similar theory is used for the sandy component and a transversely isotropic constitutive equation for the shaly component, which is assumed to possess a laminated structure. The model is first verified with experimental data and then used to obtain the properties of soils partially saturated with methanol and aviation gasoline. Finally, a GPR forward‐modelling method computes the radargrams of a typical hydrocarbon spill, illustrating the sensitivity of the technique to the type of pore‐fluid. The model and the simulation algorithm provide an interpretation methodology to distinguish different pore‐fluids and to quantify their degree of saturation.
Depth of detection of highly conducting and volume polarizable targets using induced polarization
Authors: Apparao A. , Srinivas G.S. , Subrahmanya Sarma V. , Thomas P.J. , Joshi M.S. , Rajendra Prasad P.
Published: March 2003

We define the apparent frequency effect in induced polarization (IP) as the relative difference between apparent resistivities measured using DC excitation on the one hand and high‐frequency excitation (when the IP effect vanishes) on the other. Assuming a given threshold for the minimum detectable anomaly in the apparent frequency effect, the depth of detection of a target by IP can be defined as that depth below which the target response is lower than the threshold for a given electrode array. Physical modelling shows that for the various arrays, the depth of detection of a highly conducting and volume polarizable target agrees closely with the depth of detection of an infinitely conducting and non‐polarized body of the same shape and size. The greatest depth of detection is obtained with a two‐electrode array, followed by a three‐electrode array, while the smallest depth of detection is obtained with a Wenner array when the array spread is in‐line (i.e. perpendicular to the strike direction). The depth of detection with a Wenner array improves considerably and is almost equal to that of a two‐electrode array when the array spread is broadside (i.e. along the strike direction).
What is DMO coverage?
Authors: Ferber Ralf
Published: March 2003

‘Coverage’ or ‘fold’ is defined as the multiplicity of common‐midpoint (CMP) data. For CMP stacking the coverage is consistent with the number of traces sharing a common reflection point on flat subsurface reflectors. This relationship is not true for dipping reflectors. The deficiencies of CMP stacking with respect to imaging dipping events have long been overcome by the introduction of the dip‐moveout (DMO) correction. However, the concept of coverage has not yet satisfactorily been updated to a ‘DMO coverage’ consistent with DMO stacking. A definition of constant‐velocity DMO coverage will be proposed here. A subsurface reflector will be illuminated from a given source and receiver location if the time difference between the reflector zero‐offset traveltime and the NMO‐ and DMO‐corrected traveltime of the reflection event is less than half a dominant wavelength. Due to the fact that a subsurface reflector location is determined by its zero‐offset traveltime, its strike and its dip, the DMO coverage also depends on these three parameters. For every surface location, the proposed DMO coverage consists of a 3D fold distribution over reflector strike, dip and zero‐offset traveltime.
Adaptation of prestack migration to multi‐offset ground‐penetrating radar (GPR) data
Authors: Leparoux Donatienne , Gibert Dominique , Côte Philippe
Published: March 2003

In adapting the prestack migration technique used in seismic imaging to the inversion of ground‐penetrating radar (GPR) from time‐ to depth‐sections, we show that the theoretical integral formulation of the inversion can be applied to electromagnetic problems, albeit with three assumptions. The first two assumptions concern the electromagnetic characteristics of the medium, primarily that the medium must be perfectly resistive and non‐dispersive, and the third concerns the antennae radiation pattern, which is taken to be 2D. The application of this adaptation of the inversion method is confirmed by migrating actual GPR measurements acquired on the test site of the Laboratoire Central des Ponts et Chaussées. The results show good agreement with the geometry of the structures in the medium and confirm that the possible departure from the assumption of a purely resistive medium has no visible effect on the information concerning the geometry of scattering and reflecting structures. The field experiments also show that prestack migration processing is sufficiently robust with regard to the assumption of a non‐dispersive medium. The assumption of a 2D antennae radiation pattern, however, produces artefacts that could be significant for laterally heterogeneous media. Nevertheless, where the medium is not highly laterally heterogeneous, the migration gives a clear image of the scattering potential due to the geometry of structural contrasts in the medium; the scatterers are well focused from diffraction hyperbolae and well localized. Spatial geometry has limited dimensional accuracy and positions are located with a maximum error equal to the minimum wavelength of the signal bandpass. Objects smaller than one wavelength can nevertheless be detected and well focused if their dielectric contrasts are sufficiently high, as in the case of iron or water in gneiss gravels. Furthermore, the suitability of multi‐offset protocols to estimate the electromagnetic propagating velocity and to decrease the non‐coherent noise level of measurements is confirmed. Our velocity estimation is based on the semblance calculation of multi‐offset migrated images, and we confirmed the relevance of this quantification method using numerical data. The signal‐to‐noise ratio is improved by summing multi‐offset results after the addition of random noise on measurements. Thus the adaptation of prestack migration to multi‐offset radar measurements significantly improves the resolution of the scattering potential of the medium. Limitations associated with the methods used here suggest that 3D algorithms should be applied to strongly laterally heterogeneous media and further studies concerning the waveform inversion are necessary to obtain information about the electric nature of the medium.
Evaluation of coalbed methane reservoirs from geophysical log data using an improved fuzzy comprehensive decision method and a homologous neural network
Authors: Hou J.
Published: March 2003

The evaluation of coalbed methane reservoirs using log data is an important approach in the exploration and development of coalbed methane reservoirs. Most commonly, regression techniques, fuzzy recognition and neural networks have been used to evaluate coalbed methane reservoirs. It is known that a coalbed is an unusual reservoir. There are many difficulties in using regression methods and empirical qualitative recognition to evaluate a coalbed, but fuzzy recognition, such as the fuzzy comprehensive decision method, and neural networks, such as the back‐propagation (BP) network, are widely used. However, there are no effective methods for computing weights for the fuzzy comprehensive decision method, and the BP algorithm is a local optimization algorithm, easily trapped in local minima, which significantly affect the results. In this paper, the recognition method for coal formations is developed; the improved fuzzy comprehensive decision method, which uses an optimization approach for computing weighted coefficients, is developed for the qualitative recognition of coalbed methane reservoirs. The homologous neural network, using a homologous learning algorithm, which is a global search optimization, is presented for the quantitative analysis of parameters for coalbed methane reservoirs. The applied procedures for these methods and some problems related to their application are also discussed. Verification of the above methods is made using log data from the coalbed methane testing area in North China. The effectiveness of the methods is demonstrated by the analysis of results for real log data.
Airborne EM footprints
Authors: Beamish David
Published: March 2003

As frequency‐domain airborne electromagnetic (AEM) studies move towards more detailed assessments of the near‐surface, the behaviour of system footprints, and hence the spatial averages involved in the measurement, becomes important. Published estimates suffer from two main limitations: first, they are based on perfectly conducting, thin sheet models and, secondly, they are system specific. The present study is a revision of footprint estimates based on (i) a finitely conducting half‐space and (ii) an at‐surface scale estimate that uses the spatial equivalent of the conventional electromagnetic skin depth. In order to remove the system dependence, a transmitter footprint is defined in terms of electromagnetic skin distance. Only the limiting cases of vertical and horizontal magnetic dipole sources then require analysis. Electromagnetic skin distances, two for each of the coil orientations, are defined. The revised definition makes it possible to investigate the footprint behaviour of both towed‐bird and fixed‐wing AEM systems over an altitude range from 20 to 100 m. The footprint/altitude ratio has a primary dependence on altitude and a secondary dependence on both resistivity and frequency. The analysis covers a frequency range from 1 to 100 kHz and results are presented for two specific resistivity values that represent conductive (10 Ωm) and resistive (1000 Ωm) environments. The revised footprint parameters display a quasi‐linear behaviour with altitude, particularly for mid‐range frequencies. This behaviour enables the coefficients of linear, least‐squares relationships to be obtained, thus assisting with the prediction of footprint estimates for survey planning and interpretation. A comparison of the new estimates with published values suggests that existing footprint values for a vertical magnetic dipole should be revised downward.
Biophysical stratification of the Amazon basin
Authors: Prince Stephen D. , Steininger MarC. K.
Published: March 2003

In field measurement programmes, stratified sampling can optimize sampling efficiency, but stratification is often undertaken subjectively, and is frequently based on a priori classification schemes such as those used for vegetation maps. In order to avoid the problems associated with a priori subjective schemes, we explore here an objective procedure, Regression Tree Analysis (RTA). RTA has previously been used in local‐scale studies, but here we apply it to a very large study domain, namely the entire humid tropical zone of South America. The aim of the study was to develop an optimal sampling design in preparation for the Large Scale Biosphere‐Atmosphere Experiment in Amazonia (LBA). Co‐registered spatially continuous fields of rainfall, temperature, photosynthetically active radiation (PAR), the normalized difference index (NDVI), an index of surface moisture, and other independent variables were used to predict three dependent variables, annual net radiation (Rn), latent heat (LE) and net primary production (NPP). Rather than simply dividing the study area based on differing levels of the three dependent variables, empirical models were developed using RTA to indicate how the relationships between these and possible forcing variables vary across the study area. For each variable long‐term seasonal indices such as annual average, monthly minimum and amplitude were used to exclude effects of temporal phase differences between the hemispheres. The resulting hierarchical models revealed variations in the interdependence of the forcing variables throughout the study area and therefore provided a basis for a stratified sampling and identifying the most important variables to be collected in LBA for the Amazon basin as a whole as well as optimizing the sampling scheme for scaling up findings from the field scale to larger areas.
Feedback significantly influences the simulated effect of CO2 on seasonal evapotranspiration from two agricultural species
Authors: Wilson KelL. B. , Carlson TobY. N. , Bunce James A.
Published: March 2003

The direct effect of elevated carbon dioxide on evapotranspiration over a growing season was investigated by scaling up single‐leaf gas exchange measurements on soybean and corn plants grown and measured at three carbon dioxide concentrations. Stomatal conductance decreased markedly with increasing carbon dioxide in these species under most conditions. Coupled soil–vegetation–atmosphere models were used to scale up these single‐leaf level measurements to simulate evapotranspiration at the regional scale from planting to harvest. The coupled modelling system introduced feedbacks over the season that are not present at the measurement level, which decreased the effect of carbon dioxide on evapotranspiration. Four sets of simulations were performed to evaluate specifically the magnitude of four feedbacks; two resulting from scale, surface layer and mixed layer feedback, one resulting from soil evaporation and one resulting from the interactions of stomatal conductance and the simulated canopy microclimate (physiological feedback). The feedbacks occurring from scale were consistent with previous analytical work indicating that transpiration becomes less dependent on stomatal conductance at larger scales. Evaporation from the soil has been generally neglected in past studies on carbon dioxide effects, but was especially important in decreasing the effects of carbon dioxide on evapotranspiration and showed a seasonal dynamic. The feedback resulting from physiological responses has also received less attention than the feedbacks from scale, but was only moderately important in these simulations. We also investigated the seasonal dynamics of how the observed increase in leaf area at elevated carbon dioxide affects evapotranspiration. Considering all the feedbacks and the observed increase in leaf area at elevated carbon dioxide, the simulated decrease in evapotranspiration was not negligible but was much less than the decrease in stomatal conductance. At the regional scale and maximum complexity in our model, the simulated decrease in seasonal evapotranspiration at doubled carbon dioxide (700 μmol mol–1) was 5.4% for soybeans and 8.6% for corn.