bluuebunny/crossref_metadata_2025 huggingface dataset:
A novel nuclease activity from Xenopus laevis releases short oligomers from 5′‐ends of double‐and single‐stranded DNA
Authors: Reichenberger Susanne , Brüll Nicole , Feldmann Elke , Göttlich Bernd , Vielmetter Walter , Pfeiffer Petra
Published: November 2003

Background: Double‐strand breaks in chromosomal DNA of eucaryotic cells are assumed to be repaired by mechanisms of illegitimate recombination capable of direct rejoining of the broken ends. Cell‐free extracts of Xenopus laevis eggs efficiently perform these end joining reactions with any pair of noncomplementary DNA termini whose single‐stranded 5′‐ or 3′‐overhangs do not exceed a length of ≈ 10 nt.

Results: Using hairpin‐shaped oligonucleotides that allow the construction of double‐strand break termini with 5′‐ or 3′‐overhangs of defined length and sequence we show that 5′‐overhangs of more than 9–10 nt are exonucleolytically resected in the extract to produce shorter 5′‐overhangs that can be metabolized in the end joining reaction. 5′‐recessed ends in double‐stranded DNA with 3′‐overhangs of more than 2 nt as well as the 5′‐ends of single‐stranded DNA also serve as substrates for the exonuclease activity. In all cases, oligomers of about 10 nt are released from the 5′‐ends.

Conclusions: We describe here a novel 5′‐exonuclease activity present in eggs from Xenopus laevis that reproducibly removes decameric oligonucleotides from 5′‐ends of double‐ and single‐stranded DNA. A possible function of this unusual activity is discussed in the context of homologous and illegitimate genetic recombination processes.
The analysis of complex developmental programmes: amphibian metamorphosis
Authors: Kanamori Akira , Brown Donald D.
Published: November 2003

Metamorphosis in frogs and toads is a set of complex developmental programmes controlled by thyroid hormone (TH). The pervasive and dramatic changes that occur as a tadpole turns into a frog have captured the attention of life scientists from many disciplines. For evolutionary biologists, the extent to which related organisms incorporate metamorphosis in their life cycle is of paramount interest. For specialists who study cell death, a burgeoning field of research interest, apoptosis is a major event in metamorphosis. It can be induced in many tissues, even in whole organs, by TH. For endocrinologists, TH‐induced metamorphosis is a model for the general problem of the molecular basis of TH action and the interaction of the hypothalamus, the pituitary and the thyroid glands. However, the emphasis in this essay is the use of amphibian metamorphosis to study complex developmental programmes such as vertebrate organogenesis which can be initiated by the simple addition of TH to the tadpole's rearing water.
Implications of the zinc‐finger motif found in the DNA‐binding domain of the human XPA protein
Authors: Morita Eugene H. , Ohkubo Tadayasu , Kuraoka Isao , Shirakawa Masahiro , Tanaka Kiyoji , Morikawa Kosuke
Published: November 2003

Background: The XPA (xeroderma pigmentosum group A) protein specifically recognizes the UV‐ or chemically damaged DNA lesions, and triggers the nucleotide excision repair process. This XPA protein contains the functional domain which is crucial to the recognition of damaged DNA. Its primary structure suggests that this DNA binding domain may contain a zinc‐finger motif. To gain a more detailed insight into this zinc‐finger motif, we have measured the 113Cd‐NMR spectra of the DNA binding domains derived from the wild‐type and mutant XPA proteins.

Results: 113Cd‐NMR analysis, combined with atomic absorption and site‐directed mutagenesis, revealed that the DNA binding domain contains one zinc ion, coordinated with four cysteine residues (Cys105, Cys108, Cys126, and Cys129), that is essential for correct protein folding in vivo and in vitro

Conclusions: The four ligand cysteine residues form a Cys‐X2‐Cys‐X17‐Cys‐X2‐Cys motif, which is reminiscent of the (Cys)4 type zinc‐finger motif found in numerous transcriptional regulatory proteins. However, the secondary structure prediction and the 3D‐1D compatibility analysis demonstrate that there is no structural similarity in the vicinity of the zinc‐finger motif between the XPA protein and other zinc‐finger containing proteins. We conclude that the XPA protein contains a new type of zinc‐finger motif.
Glutaminyl‐tRNA synthetase: from genetics to molecular recognition
Authors: Ibba Michael , Hong Kwang‐Won , Söll Dieter
Published: November 2003

Accurately aminoacylated tRNAs are an a priori requirement for translation of the genetic code. They are synthesized by the aminoacyl‐tRNA synthetases which select both the correct amino acid and tRNA from a total of more than 400 possible combinations. Genetic, biochemical and structural studies have begun to reveal the mechanisms by which this specificity is achieved by Escherichia coli glutaminyl‐tRNA synthetase (GlnRS). Sequence‐specific interactions between GlnRS and tRNAGln determine both the accuracy of tRNA selection and the efficiency of aminoacylation. Thus, amino acid recognition is tRNA‐dependent. Consequently, while a noncognate tRNA may be recognized by GlnRS, the resulting tRNA–enzyme complex displays a considerably reduced affinity for glutamine compared to wild‐type. This mechanism now provides a ready explanation as to why the majority of tRNA mischarging events, including those originally described over 25 years ago for GlnRS, impair cellular viability only to a limited degree.
Developmental expression of the Bombyx Antennapedia homologue and homeotic changes in the Nc mutant
Authors: Nagata Toshifumi , Suzuki Yoshiaki , Ueno Kohji , Kokubo Hiroki , Xu Xin , Hui Chi‐chung , Hara Wajiro , Fukuta Masakazu
Published: November 2003

Background: Abundant availability of homeotic mutants in Bombyx mori provides us with clues to study the body plan of the silkworm. Previous studies indicated that the ECa/ECa and EN/EN embryos, which reveal drastic morphological changes (Itikawa 1943, 1952) lack the homologue of abd‐A and the homologues of abd‐A and Ubx, respectively (Ueno et al. 1992). It will be interesting to characterize a mutant named Nc, the locus of which was mapped about 1.4 cm apart from the E loci (Itikawa 1944, 1952).

Results: In the present study we cloned and identified the Bombyx Antennapedia cDNA from a library of larval middle silk gland. The developmental expression patterns of the Bombyx Antennapedia were analysed in embryos and larval middle silk glands. We found the Bombyx Antennapedia mRNA of the Nc mutant lacks the homeobox region and its downstream region. This defect comes from a corresponding deletion on the Nc chromosome. Development of the Nc/Nc embryos terminates at stage 26, revealing a transformation of the prothoracic legs into antennae, milder changes in the mesothoracic legs, compression between the prothoracic and mesothoracic segments as well as in the gnathocephalon region, and a severe growth suppression of the silk glands.

Conclusions: These results give a molecular basis and detailed morphological abnormalities of the Nc mutant known since 1944.
Recognition mechanisms of the minus‐strand origin of phage f1 by Escherichia coli RNA polymerase
Authors: Higashitani Nahoko , Higashitani Atsushi , Guan Zhi‐Wen , Horiuchi Kensuke
Published: November 2003

Background: The primer RNA for the synthesis of the minus strand of filamentous coliphages is produced by host RNA polymerase at a specific site on the plus strand template. The mechanism used by the enzyme in recognizing the origin is unknown, but minus strand replication requires the holoenzyme form of RNA polymerase. The origin contains two inverted repeats which can form hairpins.

Results: When the origin sequence is drawn arranging the two hairpins horizontally, it resembles a stretch of a mostly double‐stranded molecule. The nucleotides protected from nucleases by the holoenzyme were found to be located in two regions on this drawing: one around the 35th nucleotide upstream of the RNA start site, and the other ranging from the 10th nucleotide upstream to the 10th downstream, of the start site. The core enzyme did not show any protection. Mutational analyses of the origin indicated that the base‐paired structure in the former region was important for origin activity. In the region around the 10th nucleotide upstream of the start site, specific base(s) in the non‐template strand were required for origin activity, while the base sequence of the template strand was irrelevant.

Conclusions: It is likely that the recognition mechanism of the origin by RNA polymerase shares common features with that of transcriptional promoters.
The N‐end rule pathway of protein degradation
Authors: Varshavsky Alexander
Published: November 2003

The N‐end rule relates the in vivo half‐life of a protein to the identity of its N‐terminal residue. Similar but distinct versions of the N‐end rule operate in all organisms examined, from mammals to fungi and bacteria. In eukaryotes, the N‐end rule pathway is a part of the ubiquitin system. Ubiquitin is a 76‐residue protein whose covalent conjugation to other proteins plays a role in many biological processes, including cell growth and differentiation. I discuss the current understanding of the N‐end rule pathway.
Chi‐activated RecBCD enzyme possesses 5′→3′ nucleolytic activity, but RecBC enzyme does not: evidence suggesting that the alteration induced by Chi is not simply ejection of the RecD subunit
Authors: Anderson Daniel G. , Churchill Jason J. , Kowalczykowski Stephen C.
Published: November 2003

Background: Homologous recombination in Escherichia coli is initiated by the RecBCD enzyme, and is stimulated by DNA elements known as Chi (χ) sites. The RecBCD enzyme is both a helicase and a nuclease. Recognition of χ causes both attenuation of the 3′→5′ exonuclease activity of the RecBCD enzyme, and activation of an exonuclease activity with 5′→3′ polarity, while leaving the helicase activity unaffected. A variety of evidence suggests that χ‐recognition by RecBCD enzyme is accompanied by ejection of the RecD subunit.

Results:Through examination of RecBCD exonuclease activity under a variety of conditions, we have shown that recognition of χ by the RecBCD enzyme results in a net reduction of nuclease activity. In addition, the exact location of the first cleavage event elicited by χ‐activation of the 5′→3′ nuclease is dependent upon the concentration of free magnesium ions. Finally, we have demonstrated that purified RecBC enzyme (i.e. without the RecD subunit) possesses no significant exonuclease activity under conditions where the χ‐modified RecBCD enzyme is an active 5′→3′ exonuclease.

Conclusions: We have shown that, despite the activation of a 5′→3′ exonuclease, recognition of χ by the RecBCD enzyme results in a net preservation of DNA. This new χ‐activated nucleolytic action shows surprising variability in the exact location of its initial cleavage. We have demonstrated that purified RecBC enzyme is not an exact analogue of the χ‐activated RecBCD enzyme, suggesting that the biochemical basis of χ‐activation is not simply ejection of the RecD subunit.
Xenopus cyclin A1 can associate with Cdc28 in budding yeast, causing cell‐cycle arrest with an abnormal distribution of nuclear DNA
Authors: Funakoshi Minoru , Sikder Hashmat , Ebihara Hiroko , Irie Kenji , Sugimoto Katsunori , Matsumoto Kunihiro , Hunt Tim , Nishimoto Takeharu , Kobayashi Hideki
Published: November 2003

Background:

Cyclins play a regulatory role in cell cycle progression, associated with cyclin‐dependent kinases. We have investigated the structure–function relationships of cyclin A, mainly using Xenopus egg extracts in vitro. To further analyse the function and structure of cyclin A in vivo, we expressed Xenopus cyclin A1 in the budding yeast Saccharomyces cerevisiae.

Results:

We herein show that vertebrate cyclin A1 can associate with endogenous Cdc28 to form histone H1 kinase. The growth of the yeast was inhibited by the expression of indestructible cyclin A1, but not by a non‐Cdk binding cyclin A1 mutant. The induction of cyclin A1 expression in yeast caused cell cycle arrest with an abnormal distribution of nuclear DNA to the daughter bud. Suppressors of the cyclin A1‐mediated growth arrest were identified as new alleles of the cdc28 mutation that reduced the binding of cyclin A1 and possessed different affinities for the cyclin–Cdc28 complexes. The temperature‐sensitivity of the cdc28 mutation was thus preferentially suppressed by the endogenous cyclins CLN2 and CLB2.

Conclusions:

These results suggest that the Cdc28 protein kinase activity mediated by vertebrate cyclin A1 may be involved in the process of nuclear movement in the yeast, and thereby affect the dependence of the M phase on the completion of the S phase through a preferential binding affinity of the cyclin–Cdc28 complex.
Double‐cleavage production of the CTL epitope by proteasomes and PA28: role of the flanking region
Authors: Shimbara Naoki , Nakajima Hiroto , Tanahashi Nobuyuki , Ogawa Kiyoko , Niwa Shin‐ichiro , Uenaka Akiko , Nakayama Eiichi , Tanaka Keiji
Published: November 2003

Background:

Proteasomes are known to produce major histocompatibility complex (MHC) class I ligands from endogenous antigens, and the γ‐interferon‐inducible proteasome activator PA28 has been thought to play an important role in the generation of immunodominant MHC ligands by proteasomes. Several attempts have been made to show that proteasomes have the ability to yield cytotoxic T lymphocyte (CTL) epitopes effectively from model polypeptides derived from viral and intracellular proteins in vitro, but their antigen processing mechanism is poorly understood.

Results:

Proteasomes produce the tumour rejection antigen precursor peptide pRL1b (SIIPGLPLSL), but not pRL1a (IPGLPLSL), bound to the H‐2Ld molecule, from synthetic peptides covering the CTL epitope. This double cleavage production of pRL1b by proteasomes seemed to depend on the length of the flanking regions adjacent to either end of the CTL epitope, in which their successive deletions caused the almost complete prevention of pRL1b excision. The newly identified PA28 collaborates with proteasomes for efficient production of pRL1b, by promoting not only single cleavage of all susceptible peptides, but also dual cleavage in some peptides harboring certain characteristic lengths.

Conclusion:

The flanking regions outside pRL1b of suitable length appear to be essential for the correct CTL epitope production, possibly functioning as anchors to trap target peptides for proteasomal degradation. We propose a novel mechanism for dual‐cleavage excision of immunodominant epitopes by proteasomes and PA28.
Polynucleotidyl transfer reactions in site‐specific DNA recombination
Authors: Mizuuchi Kiyoshi
Published: November 2003

Site‐specific DNA rearrangement reactions are widespread among organisms. They are used, for example, by vertebrates to boost immune response diversity, and in turn by parasitic organisms to evade the host immune system by surface antigen switching. Parasitic genetic elements ubiquitous to most organisms invade new host genomic sites by a variety of types of site‐specific recombination. Polynucleotidyl transfer reactions are central to these DNA recombination reactions. The recombinase of each reaction system that ‘catalyses’ such chemical reactions at specific DNA sites are apparently designed to accomplish unique DNA geometrical specificity, or delicate control over the extent or direction of the reaction, with the sacrifice of protein turnover. Here we discuss our current understanding of several issues that relate to the polynucleotidyl transfer steps in several of the better studied site‐specific recombination reactions.
Essential role for ERK2 mitogen‐activated protein kinase in placental development
Authors: Hatano Naoya , Mori Yoshiko , Oh‐hora Masatsugu , Kosugi Atsushi , Fujikawa Takahiko , Nakai Naoya , Niwa Hitoshi , Miyazaki Jun–ichi , Hamaoka Toshiyuki , Ogata Masato
Published: November 2003

Background:  Extracellular signal‐regulated kinase 2 (ERK2) has been implicated in cell proliferation, differentiation, and survival. However, its role in vivo remains to be determined.

Results:  Here we show that the targeted disruption of the mouse ERK2 gene results in embryonic lethality by E11.5 and severe abnormality of the placenta. In these animals, the labyrinthine layer of the placenta is very thin and few foetal blood vessels are observed. ERK2 mutants can be rescued by the transgenic expression of ERK2, demonstrating that these abnormalities are caused by ERK2‐deficiency. Although ERK2‐deficient fetuses are much smaller than wild‐type littermates, this seems to be secondary to malfunction of the placenta. When the placental defect is rescued by tetraploid‐aggregation, ERK2‐deficient foetuses grow as well as littermate controls.

Conclusion:  These observations indicate that ERK2 is essential for placental development and suggest that ERK2 in the trophoblast compartment may be indispensable for the vascularization of the labyrinth.
Cks1 is degraded via the ubiquitin‐proteasome pathway in a cell cycle‐dependent manner
Authors: Hattori Takayuki , Kitagawa Kyoko , Uchida Chiharu , Oda Toshiaki , Kitagawa Masatoshi
Published: November 2003

Background:  Recent work has demonstrated the role of cdc kinase subunit 1 (Cks1) in the ubiquitin‐proteasome dependent degradation of CDK inhibitor p27Kip1 protein as an essential cofactor for SCFSkp2 ubiquitin ligase. Although over‐expression of Cks1 protein as well as it of Skp2 might be associated with tumour progression via p27Kip1 protein degradation, it is unknown how the cellular level of Cks1 is regulated.

Results:  Here we show that Cks1 protein is degraded via the ubiquitin‐proteasome pathway. Degradation of Cks1 protein was markedly inhibited by proteasome inhibitors. In addition, Cks1 protein was modified with polyubiquitin chains both in vivo and in vitro. Furthermore, we found that degradation of Cks1 protein via the ubiquitin‐proteasome pathway was facilitated in M phase during the cell cycle.

Conclusion:  These observations suggest that the level of expression of Cks1 protein is regulated at not only the transcriptional level but also the post‐translational level via the ubiquitin‐proteasome pathway in a cell‐cycle‐dependent manner.
Over‐expression of a novel nuclear interactor of Suppressor of fused, the Drosophila myelodysplasia/myeloid leukaemia factor, induces abnormal morphogenesis associated with increased apoptosis and DNA synthesis
Authors: Fouix Sylvaine , Martin‐Lannerée Séverine , Sanial Matthieu , Morla Luciana , Lamour‐Isnard Claudie , Plessis Anne
Published: November 2003

Background:  In Drosophila and vertebrates, suppressor of fused (Su(fu)) proteins act as negative regulators of the Gli/Ci transcription factors, which mediate the transcriptional effects of Hh signalling.

Results:  We sought for novel partners of Su(fu) in fly using the two‐hybrid method. Most of the Su(fu) interactors thus identified are (or are likely to be) able to enter the nucleus. We focused on one of these putative partners, dMLF, which resembles vertebrate myelodysplasia/myeloid leukaemia factors 1 and 2. We demonstrate that dMLF binds specifically to Su(fu) in vitro and in vivo. Using a novel anti‐dMLF antibody, we showed, that dMLF is a nuclear, chromosome‐associated protein. We over‐expressed a dMLF transgene in fly using an inducible expression system and showed that dMLF over‐expression disrupts normal development, leading to either a lethal phenotype or adult structural defects associated with apoptosis and increased DNA synthesis. Furthermore, the dMLF‐induced eye phenotype is enhanced by the loss of Su(fu) function, suggesting a genetic interaction between Su(fu) and dMLF.

Conclusion:  We propose that dSu(fu) and dMLF act together at the transcriptional level to coordinate patterning and proliferation during development.
Sex in the footprint bed
Authors: Tresise Geoffrey
Published: November 2003

Many animals show sexual dimorphism, one sex being consistently larger and heavier than the other. No doubt, examples of the same phenomenon also occur in the fossil record, but they may be difficult to spot and even more difficult to prove. The problems are greater still when considering trace fossils such as footprints. Even so, there seems reason to believe that some types of footprint do show sexual dimorphism.
Al Wahbah volcanic explosion crater, Saudi Arabia
Authors: Grainger David J.
Published: November 2003

Al Wahbah, on Harrat Kishb, is the most spectacular of several volcanic explosion craters found on the lava fields of western Saudi Arabia. A Quaternary phreatic event drilled out a crater 2 km in diameter through Proterozoic basement rocks and Quaternary lava flows. The crater is rimmed with a tuff ring of debris from the explosion, around which were diverted Holocene basaltic lavas.
Radon –in Northamptonshire?
Authors: SUTHERLAND SHARMAN DIANA, GLENN
Published: November 2003

With the new BGS Radon Potential Map of Great Britain published, we focus on Northamptonshire, where reports in 1988 of finding the radioactive gas in houses sent shock waves through the local community – and aroused the interest of Leicester University geologists. With the help of local authorities, research has established the main source as the Northampton Sand Formation, at the base of which is a layer of phosphatic pebbles that are relatively rich in uranium. From more than 3000 field measurements over all rocks, a geologically defined Radon Hazard Map of the county has been compiled.
Gibraltar woman and Neanderthal Man
Authors: ROSE EDWARD P.F. , STRINGER CHRISTOPHER B.
Published: November 2003

Forbes' Quarry, on the Rock of Gibraltar, yielded a human skull in 1848, one of the earliest Neanderthal skeletal remains known to science. Fragments of a second Gibraltar skull, that of a child, were described from Devil's Tower rock shelter in 1928 and have recently been reconstructed and reinterpreted to emphasize the distinction of Homo neanderthalensis from H. sapiens. Neanderthal skeletal remains are confined to Europe, the Middle East and central Asia, their most recent occurrence arguably a refugium in southern Iberia. The race seemingly became extinct about 30 000 years Before Present, for reasons as yet unknown, but a programme of excavations in Gorham's and Vanguard caves on Gibraltar is in progress to elucidate palaeoenvironmental and behavioural changes as some of the last Neanderthals were succeeded stratigraphically by anatomically modern humans with an Upper Palaeolithic culture.
FRACTURE CHARACTERIZATION FROM NEAR‐OFFSET VSP INVERSION
Authors: Horne Steve , MacBeth Colin , Queen J. , Rizer W. , Cox V.
Published: November 2003

A global optimization method incorporating a ray‐tracing scheme is used to invert observations of shear‐wave splitting from two near‐offset VSPs recorded at the Conoco Borehole Test Facility, Kay County, Oklahoma. Inversion results suggest that the seismic anisotropy is due to a non‐vertical fracture system. This interpretation is constrained by the VSP acquisition geometry for which two sources are employed along near diametrically opposite azimuths about the well heads. A correlation is noted between the time‐delay variations between the fast and slow split shear waves and the sandstone formations.
A joint inversion algorithm to process geoelectric and surface wave seismic data. Part II: applications
Authors: Misiek R. , Liebig A. , Gyulai A. , Ormos T. , Dobroka M. , Dresen L.
Published: November 2003

Seismic and geoelectric methods are often used in the exploration of near‐surface structures. Generally, these two methods give, independently of one other, a sufficiently exact model of the geological structure. However, sometimes the inversion of the seismic or geoelectric data fails. These failures can be avoided by combining various methods in one joint inversion which leads to much better parameter estimations of the near‐surface underground than the independent inversions.  In the companion paper (Part I: basic ideas), it was demonstrated theoretically that a joint inversion, using dispersive Rayleigh and Love waves in combination with the well‐known methods of DC resistivity sounding, such as Schlumberger, radial dipole‐dipole and pole‐pole arrays, provides a better parameter estimation.  Two applications are shown: a five layer structure in Borsod County, Hungary, and a three‐layer structure in Thüringen, Germany. Layer thicknesses, wave velocities and resistivities are determined. Of course, the field data sets obtained from the ‘real world’ are not as complete and as good as the synthetic data sets in the theoretical Part I.  In both applications, relative model distances, in percentages, serve as quality control factors for the different inversions; the lower the relative distance, the better the inversion result.  In the Borsod field case, Love wave group slowness data and Schlumberger, radial dipole‐dipole and pole‐pole (i.e two‐electrode) data sets are processed. The independent inversion performed using the Love wave data leads to a relative model distance of 155%. An independent Schlumberger inversion results in 41%, a joint geoelectric inversion of all data sets in 15%, a joint inversion of Love wave data and all geoelectric data sets in 15% and the robust joint inversion of Love wave data and the three geoelectric data sets in 10%.  In the Thüringen field case, only Rayleigh wave group slowness data and Schlumberger data were available. The independent inversion using Rayleigh wave data results in a relative model distance of 19%. The independent inversion performed using Schlumberger data leads to 34%, the joint and robust joint inversion of Rayleigh wave and Schlumberger data gave results of 18% and 20%, respectively.
Observations of borehole‐source amplitude reduction due to casing
Authors: Gibson Richard L. , Turpening Walter R. , Born Andrea , Turpening Roger M.
Published: November 2003

Theoretical results show that the amplitude of a borehole source is reduced when the well in which it is operated is cased and cemented. This reduction is a strong function of the formation velocity and is more weakly dependent on the direction of propagation of the wave travelling from source to receiver and on the diameter of the borehole itself. We have tested these predictions with data gathered in a cross‐hole seismic experiment conducted in two stages in 1990 and 1991. The source and receivers were located in the MIT/Stech 1‐21A and MIT/Burch 1‐20B wells at the Earth Resources Laboratory (ERL) test site in Michigan (USA). Though the source well (MIT/Stech 1‐21A) was uncased in 1990, a steel casing and cement were added prior to the collection of data in 1991. Several receiver positions were reoccupied to compare data collected with the source in open and cased holes. Using a velocity model for this area and borehole diameter measurements from a calliper log, a compensation factor can be computed that will adjust the data collected in 1991 to have amplitudes comparable to that collected in the first stage of the experiment. The accuracy of the results demonstrates the validity of the theory, which can be very useful in better understanding seismic waveforms recorded in cross‐hole experiments.
Detecting lateral resistivity inhomogeneities with the Schlumberger array
Authors: Morris Marian , Rønning Jan Steinar , Lile Ole Bernt
Published: November 2003

A method of detecting lateral resistivity inhomogeneities with a multi‐electrode cable for the Schlumberger array is presented. Using such a cable system, two dipole‐dipole soundings are gathered in addition to the Schlumberger sounding at each point. Offset differences calculated from the dipole‐dipole data give qualitative information about lateral resistivity inhomogeneities. Results from 1D modelling can give quantitative information about the 2D resistivity distribution since the dipole‐dipole soundings are made to either side of the Schlumberger sounding point. Examples from two different locations in Norway are shown. At Reinøya, northern Norway, a dipping layer, confirmed by refraction seismic data, was identified. In a sedimentary basin with a contamination plume at Haslemoen, southern Norway, the method has revealed lateral variations in resistivity. In both cases, the Schlumberger soundings could be fitted with a 1D resistivity model.
Resistivity and IP modelling of an anisotropic body located in an isotropic environment
Authors: Eskola L. , Hongisto H.
Published: November 2003

A solution based on Tabarovskii's coupled pair of surface integral equations is given for the potential of a direct current flowing in an electrically anisotropic body and within the enclosing isotropic surroundings. The sources of the secondary potential exterior and interior to the body are fictitious surface charge distributions. The equations are solved numerically using point matching with pulse functions as subsectional basis functions. The model used in the applications is a long prism, excited by long line current electrodes aligned parallel to the strike. The strike length is set at a length sufficient to guarantee 2D behaviour of the model.  Comparisons of computation results indicate that for the models, electrode arrays and numerical procedures applied, the solutions based on fictitious surface sources converge faster and behave more regularly than those based on real surface charges. When compared with previously published integral equation solutions, the present solution seems to be relatively efficient, even in the case of purely isotropic models. The model experiments also showed that at moderate resistivity contrasts, the anomaly shapes are strongly dependent on the directions of the principal axes of the body resistivity. However, when the external resistivity is more than 100 times that of the geometric mean of the principal resistivities in the body, with the principal resistivities differing from each other by at most one order of magnitude, the contribution of the anisotropy to the anomaly diminishes as a result of electrical saturation.
Depth of detection of buried resistive targets with some electrode arrays in electrical prospecting
Authors: Apparao A. , Sivarama Sastry R. , Subrahmanya Sarma V.
Published: November 2003

Assuming the minimum detectable anomaly to be 10%, depths of detection of a 2D vertical resistive sheet of thickness t are found to be 4.0t, 3.0t, 4.0t and 4.0t with Wenner, two‐electrode, three‐electrode and dipole‐dipole (β‐Wenner) arrays, respectively, when the array spread is in‐line. On the other hand, the depths of detection obtained with a broadside spread of the arrays right over the sheet are much less and are correspondingly 2.5t, 2.0t, 2.5t and 2.5t. An increase in the depth extent W of the sheet from 10t to 20t does not increase its depth of detection with the arrays.  The depths of detection of an infinitely resistive horizontal cylinder of radius R are respectively 1.5R, 1.8R, 2.0R and 2.0R with the above‐listed arrays when the array spread is in‐line. With broadside spread of any of the arrays, the depth of detection is seen to be 2.5R.  In the case of a spherical target of radius R, the detection depths of any of the arrays are found to be small and to vary between 0.8R and 1.1R.  Comparatively, the detection depths of resistive targets are much lower than those of conductive targets of the same size and shape, with any electrode array. Among all the arrays studied, the two‐electrode array performs worst in the detection of resistive targets while it performs best in detecting conducting targets of limited lateral extent. In the case of a spherical target, either resistive or conductive, there is no distinct change in its detection depth with array.
Inversion of potential field data by genetic algorithms
Authors: Boschetti Fabio , Dentith Mike , List Ron
Published: November 2003

We present a genetic algorithm that simultaneously generates a large number of different solutions to various potential field inverse problems. It is shown that in simple cases a satisfactory description of the ambiguity domain inherent in potential field problems can be efficiently obtained by a simple analysis of the ensemble of solutions. From this analysis we can also obtain information about the expected bounds on the unknown parameters as well as a measure of the reliability of the final solution that cannot be recovered with local optimization methods. We discuss how the algorithm can be modified to address large dimensional problems. This can be achieved by the use of a ‘pseudo‐subspace method’, whereby problems of high dimensionality can be globally optimized by progressively increasing the complexity and dimensionality of the problem as well as by subdividing the overall calculation domain into a number of small subdomains. The effectiveness and flexibility of the method is shown on a range of different potential field inverse problems, both in 2D and 3D, on synthetic and field data.
A physical study of low‐frequency dispersion of rock conductivity in time‐domain electromagnetics
Authors: Kamenetsky Felix M. , Novikov Peter V.
Published: November 2003

Most rocks display conductivity dispersion in the low‐frequency range, when the usual displacement currents are neglected. The strong influence this low‐frequency dispersion (LFD), including the response sign reversals, was revealed by field experiments with the coincident‐loop configuration widely used in transient electromagnetics (EM). Mathematical modelling of LFD has been the subject of numerous studies. However, confirmation of the role of LFD or induced polarization (IP) by comparing mathematical modelling and field data is rather poor, because knowledge of the properties of rocks in the area of the field measurements is usually insufficient. For this reason physical modelling of LFD has been carried out at Moscow State Geological‐prospecting Academy (Russia) in 1994‐95. In order to observe criteria of similarity for both induction and polarization transients, a ring‐shaped model was chosen and was represented by an electric circuit, consisting of lumped elements (real rock samples included). Qualitatively different transients for dispersive models and their non‐dispersive ohmic equivalents were observed.
Elimination of source‐generated noise from correlated vibroseis data (the ‘ghost‐sweep’ problem)
Authors: Polom Ulrich
Published: November 2003

The most common noise‐reduction methods employed in the vibroseis technique (e.g. spike and burst reduction, vertical stacking) are applied in the field to reduce noise at a very early stage. In addition, vibrator phase control systems prevent signal distortions produced by non‐linearity of the source itself. However, the success of these automatic correction methods depends on parameter justification by the operator and the actual characteristics of the distorting noise. More specific noise‐reduction methods (e.g. Combisweep (Trade mark of Geco‐Prakla), elimination of harmonics) increase production costs or need uncorrelated data for the correction process. Because the field data are usually correlated and vertically stacked in the field to minimize logistical and processing costs, it is not possible to make subsequent parameter corrections to optimize the noise reduction after correlation and vertical stacking of a production record.

The noise‐reduction method described here uses the final recorded, correlated and stacked vibroseis field data. This method eliminates signal artifacts caused e.g. by incorrect vibroseis source signals being used in parameter estimation when a frequency–time analysis is combined with a standard convolution process. Depending on the nature of the distortions, a synthetically generated, nearly recursive noise‐separation operator compresses the noise artifact in time using a trace‐by‐trace filter. After elimination of this compressed noise, re‐application of the separation operator leads to a noise‐corrected replacement of the input data. The method is applied to a synthetic data set and to a real vibroseis field record from deep seismic sounding, with good results.
Anisotropic migration of coincident VSP and cross‐hole seismic reflection surveys
Authors: Rowbotham Peter S.
Published: November 2003

Seismic depth migration may result in false reflector positioning and destructive interference when an incorrect velocity field is used to convert from time to depth. The assumption of isotropy to describe anisotropic rocks is one major source of error in the velocity model, although individual survey images may not be impaired by such an approximation. When different survey types such as VSP and cross‐hole reflection seismics have coincident illumination of the subsurface, it is important not only to produce consistent images upon depth migration, but also to determine a consistent velocity model. Using real data sets as examples, both objectives are successfully achieved when anisotropy is incorporated into the velocity model.
Complex polynomials for the computation of 2D gravity anomalies
Authors: Oliva Sergio E. , Ravazzoli Claudia L.
Published: November 2003

We present an efficient algorithm using a complex variables formulation for the computation of the gravity effect of 2D polygonal bodies having densities varying both laterally and with depth. The first derivatives of the gravity effect are also provided in order to enable the computation of the Jacobian matrix, which is necessary for linear inverse gravity problems. A geophysical example based on numerical assumptions about the density contrast on a well‐studied basin area shows the applicability of the algorithm.
Theoretical study of slope effects in resistivity surveys and applications
Authors: Sahbi H. , Jongmans D. , Charlier R.
Published: November 2003

When electric soundings are made over an irregular terrain, topographic effects can influence the values of apparent resistivity and lead to erroneous 1D interpretation. A 3D finite‐element method has been applied to study the topographical effect of a slope on Schlumberger soundings parallel to the strike. When the resistivity survey is performed at the top of the slope, the apparent resistivity values can be two times higher than in the flat‐earth case, depending on the angle (α) and height (H) of the slope, and on the distance (X) between the sounding and the slope top. The results are presented as nondimensional curves which can be used for evaluating topographic anomalies for any value of the parameters α, H and X. It is numerically shown that the topographic effects can be removed from measurements on horizontally layered structures with an irregular earth surface. Real measurements were performed in different geological conditions over an irregular terrain. The correction method based on the nondimensional curves has been applied to the data and has enabled the determination of the correct layered ground configuration using 1D interpretation.
Modelling the 2D terrain effect on MT by the boundary‐element method
Authors: Xu Shi‐zhe , Zhou Hui
Published: November 2003

The boundary‐element method is used to model the 2D terrain effect on the magnetotelluric (MT) field. Firstly, the boundary‐value problem of a 2D magnetotelluric field is transformed into an integral equation problem by using Green's theorem. Then the boundary‐element method is used to solve the integral equation and to obtain the MT field and its normal derivative on the terrain. From these values, the apparent resistivity can be calculated.

 Compared with the finite‐element method, the boundary‐element method is simpler in element division and the initial data preparation. The configuration of a terrain divided by the boundary‐element method is more consistent with the practical terrain. The method proposed in this paper can be run on a microcomputer, so that it can be used in the field.
One‐dimensional magnetotelluric inversion using an adaptation of Zohdy's resistivity method
Authors: Hobbs B.A. , Dumitrescu C.C.
Published: November 2003

An iterative refinement method for determining a layered resistivity model from a Schlumberger or Wenner sounding curve is adapted to determine a layered resistivity model by using apparent resistivity and phase derived from the magnetotelluric impedance. Magnetotelluric observations presented as a function of period are first converted to an approximate resistivity–depth profile using Schmucker's transformation and this is used to construct an initial guess (starting) model. A two‐stage procedure is then invoked. Keeping resistivities constant, layer boundaries are first adjusted to give a minimum misfit between measured data and responses and this is followed by resistivity adjustments with fixed layer boundaries to reduce the misfit further. The method is illustrated by application to some synthetic data both exact and with added noise, to a real field data set and to some magnetotelluric profile data obtained in a survey over the Carnmenellis granites in south Cornwall. The method is validated by recovering conductivity models from the exact and noisy 1D synthetic data. For complicated three‐dimensional data at a single site and along a profile of stations, the method is shown to produce acceptable solutions which may be used as starting models in further two‐ or three‐dimensional studies.
A generalized concept of resultant gradient to interpret potential field maps
Authors: Shaw R.K. , Agarwal B.N.P.
Published: November 2003

The existing concept of the gradient of the potential field anomaly over a 3D source has been generalized. An observed anomaly is modified through a filter based on an assumed source geometry. The first‐order derivatives of this modified anomaly in three mutually orthogonal directions form the components of a vector termed the resultant gradient. The gravity anomaly over a point mass, a vertical line mass and the gravity/magnetic anomaly reduced‐to‐pole over a bottomless right rectangular prism have been suitably modified to yield a specific shape for the amplitude of the resultant gradient in order to decipher the depth of the source centroid/corner. The applicability of the proposed technique is demonstrated by the analyses of a simulated example over a composite source and a real example from published literature with drill‐hole information.
Variation in growth stimulation by elevated carbon dioxide in seedlings of some C3 crop and weed species
Authors: BUNCE JAMES
Published: November 2003

Seven C3 crop and three C3 weed species were grown from seed at 360 and at 700 cm3 m–3 carbon dioxide concentrations in a controlled environment chamber to compare dry mass, relative growth rate (RGR), net assimilation rate (NAR), leaf area ratio (LAR) and photosynthetic acclimation at ambient and elevated carbon dioxide. The dry mass at the final harvest at elevated carbon dioxide relative to that at ambient carbon dioxide was highly correlated with the RGR at the lower carbon dioxide concentration. This relationship could be quite common, because it does not require that species differ in the response of RGR or photosynthesis to elevated carbon dioxide, and holds even when species differ moderately in these responses. RGR was also measured for a limited period at the end of the experiment to determine relationships with leaf gas exchange measured at this time. Relative increases in RGR at elevated carbon dioxide at this time were more highly correlated with the relative increase in NAR at elevated carbon dioxide than with the response of LAR. The amount of acclimation of photosynthesis was a good predictor of the relative increase in NAR at elevated carbon dioxide, and the long‐term increase in photosynthesis in the growth environment. No differences between crops and weeds or between cool and warm climate species were found in the responses of growth or photosynthetic acclimation to elevated carbon dioxide.
Potential for carbon sequestration in European soils: preliminary estimates for five scenarios using results from long‐term experiments
Authors: SMITH PETE , POWLSON DAVID , GLENDINING MARGARET , SMITH JO
Published: November 2003

One of the main options for carbon mitigation identified by the IPCC is the sequestration of carbon in soils. In this paper we use statistical relationships derived from European long‐term experiments to explore the potential for carbon sequestration in soils in the European Union. We examine five scenarios, namely (a) the amendment of arable soils with animal manure, (b) the amendment of arable soils with sewage sludge, (c) the incorporation of cereal straw into the soils in which it was grown, (d) the afforestation of surplus arable land through natural woodland regeneration, and (e) extensification of agriculture through ley‐arable farming. Our calculations suggest only limited potential to increase soil carbon stocks over the next century by addition of animal manure, sewage sludge or straw ( 15 Tg C y–1), but greater potential through extensification of agriculture (≈ 40 Tg C y–1) or through the afforestation of surplus arable land (≈ 50 Tg C y–1). We estimate that extensification could increase the total soil carbon stock of the European Union by 17%. Afforestation of 30% of present arable land would increase soil carbon stocks by about 8% over a century and would substitute up to 30 Tg C y–1 of fossil fuel carbon if the wood were used as biofuel. However, even the afforestation scenario, with the greatest potential for carbon mitigation, can sequester only 0.8% of annual global anthropogenic CO2‐carbon. Our figures suggest that, although efforts in temperate agriculture can contribute to global carbon mitigation, the potential is small compared to that available through reducing anthropogenic CO2 emissions by halting tropical and sub‐tropical deforestation or by reducing fossil fuel burning.
Changes in carbon isotope discrimination in grain cereals from different regions of the western Mediterranean Basin during the past seven millennia. Palaeoenvironmental evidence of a differential change in aridity during the late Holocene
Authors: ARAUS J.L. , FEBRERO A. , BUXO R. , CAMALICH M.D. , MARTIN D. , MOLINA F. , RODRIGUEZ‐ARIZA M.O. , ROMAGOSA I.
Published: November 2003

Carbon isotope discrimination (Δ) was determined for kernels of six‐row barley and durum wheat cultivated in the western Mediterranean basin during the last seven millennia. Samples came from different archaeological sites in Catalonia (north‐east Spain) and in the south‐east of Spain (mainly eastern Andalusia). Samples from the present were also analysed. Mean values of Δ for barley and durum wheat grains decreased slightly from Neolithic (7000–5000 BP) to Chalcolithic‐Bronze (5000–3000 BP) and Iron ages (3000–2200 BP) both in Catalonia and in south‐east (SE) Spain. Values were consistently lower in SE Spain than in Catalonia throughout these five millennia, which suggests that Catalonia was less arid than SE Spain in this period. Within a given region, current discrimination values for kernels of the same cereal species cultivated under rainfed conditions were lower than those of archaeological grains, which implies more arid conditions at present. Furthermore, an empirical relationship between Δ of mature kernels and total precipitation (plus irrigation where applicable) during grain filling (r2 = 0.73, N = 25) was established for barley, currently cultivated at different locations in the western Mediterranean basin in Spain. The resulting relationship was applied to the Δ data for barley kernels from 10 archaeological sites in Catalonia and 10 sites in SE Spain, to estimate the precipitation during grain filling at the time the kernels were produced. For both regions, current climatic conditions are consistently more arid than those inferred for the Neolithic, Bronze and Iron ages. In addition, although Catalonia was estimated to have had consistently wetter conditions (about 20% more precipitation) than SE Spain throughout these millennia, differences in precipitation between these two regions have recently increased, with 79% more precipitation in Catalonia. Results indicate a more rapid increase in aridity in SE Spain than in Catalonia, probably produced during the last few centuries, and due to anthropogenic causes.