bluuebunny/crossref_metadata_2025 huggingface dataset:
Defect in cytokinesis of fission yeast induced by mutation in the WD40 repeat motif of a TFIID subunit
Authors: Yamamoto Tohru , Horikoshi Masami
Published: March 2003

Background:

TBP‐associated factors contain a variety of structural motifs and their related in vivo significance has remained unclear. We have attempted to identify specific biological phenomena linked to a particular domain of a TAF by analysing domain‐exchanged chimeric mutants between Schizosaccharomyces pombe (Sp) and Saccharomyces cerevisiae (Sc) counterparts.

Results:

Contrary to the case of TBP, Sp TAF containing the WD40 repeat cannot be exchanged for its Sc counterpart, despite their highly conserved primary structures. This ‘species‐specific’ function locates in the N‐terminal region. The C‐terminal region, largely consisting of the WD40 repeat, is exchangeable for the corresponding region of its Sc counterpart. Growth of the strain harbouring this C‐terminal chimeric mutant is temperature‐sensitive. The chimeric gene product did not disappear at a restrictive temperature, a finding which strongly suggests that the growth defect is caused by an aberration in the interactions through the WD40 repeat structural motif. With temperature elevation, the chimeric mutants underwent drastic morphological changes due to a defect in cytokinesis.

Conclusions:

The WD40 repeat of TAF is primarily involved in reactions which might regulate cytokinesis in Sp.
Axin, an inhibitor of the Wnt signalling pathway, interacts with β‐catenin, GSK‐3β and APC and reduces the β‐catenin level
Authors: Nakamura Tsutomu , Hamada Fumihiko , Ishidate Takao , Anai Ken‐ichi , Kawahara Kohichi , Toyoshima Kumao , Akiyama Tetsu
Published: March 2003

Background:

The Wnt/Wingless signalling pathway plays an important role in both embryonic development and tumorigenesis. β‐Catenin and Axin are positive and negative effectors of the Wnt signalling pathway, respectively.

Results:

We found that Axin interacts with β‐catenin and glycogen synthase kinase‐3β (GSK‐3β). Furthermore, the regulation of the G‐protein signalling (RGS) domain of Axin is associated with the colorectal tumour suppressor adenomatous polyposis coli (APC). Overexpression of Axin in the human colorectal cancer cell line SW480 induced a drastic reduction in the level of β‐catenin. Interaction with β‐catenin and GSK‐3β was required for the Axin‐mediated β‐catenin reduction.

Conclusion:

Axin interacts with β‐catenin, GSK‐3β and APC, and negatively regulates the Wnt signalling pathway, presumably by regulating the level of β‐catenin.
Post‐transcriptional control of the level of mRNA by hepatitis B virus X gene in the transient expression system using human hepatic cells
Authors: Shimazu Tsutomu , Takada Shinako , Ueno Yoshio , Hayashi Yasuyuki , Koike Katsuro
Published: March 2003

Background

Hepatitis B virus (HBV) infection is closely related to the development of not only acute or chronic hepatitis, but also hepatocellular carcinoma. Among the HBV genes, the X gene has been implicated in the carcinogenicity of this virus as a major causative factor by its ability to activate viral and cellular genes in trans via protein–protein interaction with cellular factors without binding to DNA.

Results

To explore the possibility of other functions of the X gene, we examined the effect of X protein on the transient expression system of simian virus 40 (SV40) large T‐antigen or chloramphenicol acetyltransferase (CAT) mRNA using SV40 promoter or EF‐1α (human elongation factor 1α) promoter, by co‐transfecting an X gene expression plasmid to human hepatic cell lines, HepG2 and Huh7. In contrast to the SV40 promoter‐mediated expression, the level of both T‐antigen and CAT mRNAs expressed from the EF‐1α promoter was strikingly decreased by X protein in both hepatic cells. The nuclear run‐on assay and the mRNA decay experiment using actinomycin D, indicated that the effect of X protein on the lowering of the level of chimeric mRNA was due to the degradation of mRNA, but not repression of transcriptional initiation. Moreover, this effect was dependent on the 22 bp sequence in the 5′ untranslated region of mRNA derived from the EF‐1α promoter.

Conclusion

The present data suggest a new function of the X gene to post‐transcriptionally control the stability of mRNA through the 5′ untranslated region derived from the EF‐1α promoter in human hepatic cells.
Isolation and characterization of cortactin isoforms and a novel cortactin‐binding protein, CBP90
Authors: Ohoka Yoshiharu , Takai Yoshimi
Published: March 2003

Background

Cortactin is a major phosphotyrosyl protein in pp60v–src‐transformed chicken embryo cells. Cortactin binds to actin filament (F‐actin) through a unique region which consists of six tandem 37 amino acid repeats, named cortactin repeats. Furthermore cortactin has one src homology 3 (SH3) domain.

Results

In this study we have isolated two new isoforms of cortactin from the rat brain using a polymerase chain reaction (PCR) method, and have named the original cortactin as cortactin‐A and the newly isolated forms as cortactin‐B and ‐C. Cortactin‐A, ‐B and ‐C had six, five, and four cortactin repeats, respectively. All the isoforms were able to bind to F‐actin, but only cortactin‐A demonstrated an F‐actin‐crosslinking activity. In addition, cortactin‐A was able to bind along the side of F‐actin. Next, using a blot overlay assay with glutathione S‐transferase (GST)‐cortactin‐A, we identified a cortactin‐A‐binding protein with an Mr of ≈90 kDa in rat brain and named it CBP90 (cortactin‐binding protein with an Mr of ≈90 KDa). CBP90 was purified from rat brain and its cDNA was cloned from a rat brain cDNA library. The deduced amino acid sequence of CBP90 had no significant similarity to any other protein, but it had a proline‐rich domain at the C‐terminal region. CBP90 was able to bind to all the cortactin isoforms. A deletion mutant analysis of cortactin‐A and CBP90 revealed that the SH3 domain of cortactin‐A was able to bind to the proline‐rich region of CBP90. A Western blot analysis with an anti‐CBP90 antibody indicated that, among the rat tissues examined, CBP90 was exclusively expressed in brain. Furthermore, its subcellular distribution and developmental expression patterns were similar to those of cortactin.

Conclusion

These results suggest that cortactin interacts with CBP90 and plays a role in regulation of the actin cytoskeleton in brain.
Role of Bcl‐2 family proteins in apoptosis: apoptosomes or mitochondria?
Authors: Tsujimoto Yoshihide
Published: March 2003

Apoptosis is an essential physiological process for the selective elimination of cells, which is involved in a variety of biological events. The Bcl‐2 family is the best characterized protein family involved in the regulation of apoptotic cell death, consisting of anti‐apoptotic and pro‐apoptotic members. The anti‐apoptotic members of this family, such as Bcl‐2 and Bcl‐xL, prevent apoptosis either by sequestering proforms of death‐driving cysteine proteases called caspases (a complex called the apoptosome) or by preventing the release of mitochondrial apoptogenic factors such as cytochrome c and AIF (apoptosis‐inducing factor) into the cytoplasm. After entering the cytoplasm, cytochrome c and AIF directly activate caspases that cleave a set of cellular proteins to cause apoptotic changes. In contrast, pro‐apoptotic members of this family, such as Bax and Bak, trigger the release of caspases from death antagonists via heterodimerization and also by inducing the release of mitochondrial apoptogenic factors into the cytoplasm via acting on mitochondrial permeability transition pore, thereby leading to caspase activation. Thus, the Bcl‐2 family of proteins acts as a critical life–death decision point within the common pathway of apoptosis.
The biochemistry and biological significance of nonhomologous DNA end joining: an essential repair process in multicellular eukaryotes
Authors: Lieber Michael R.
Published: March 2003

Recent progress over the past year has provided new insights into the proteins involved in nonhomologous end joining. The assembly of Ku and DNA‐dependent protein kinase at DNA ends is now understood in greater detail. Murine genetic knockouts for DNA ligase IV and XRCC4 are embryonic lethal, indicating that nonhomologous end joining is essential for viability. Interestingly, neurones, in addition to lymphocytes, are particularly vulnerable to an absence of NHEJ.
Abnormalities of developmental cell death in Dad1‐deficient mice
Authors: Nishii Kiyomasa , Tsuzuki Teruhisa , Kumai Madoka , Takeda Naoki , Koga Hideya , Aizawa Shinichi , Nishimoto Takeharu , Shibata Yosaburo
Published: March 2003

Background

Dad1, the defender against apoptotic cell death, comprises the oligosaccharyltransferase complex and is well conserved among eukaryotes. In hamster BHK21‐derived tsBN7 cells, loss of Dad1 causes apoptosis which cannot be prevented by Bcl‐2.

Results

To determine the role of Dad1 function in vivo, we prepared by gene targeting, mice harbouring a disrupted Dad1 gene. Homozygous mutants died shortly after they were implanted with the characteristic features of apoptosis. In an in vitro blastocyst culture system, Dad1‐null cells displayed abnormalities which were comparable to those obtained in vivo. However, oligosaccharyltransferase activity was apparently retained even after the Dad1‐null cells were destined to die. Some live‐born heterozygous mutants displayed soft‐tissue syndactyly. Mild thymic hypoplasia was also indicated in heterozygotes.

Conclusion

These results suggest the involvement of the Dad1 gene in the acquisition of a common syndactyly phenotype, as well as in the control of programmed cell death during development.
Triggering of neuronal cell death by accumulation of activated SEK1 on nuclear polyglutamine aggregations in PML bodies
Authors: Yasuda Shingo , Inoue Kiyoshi , Hirabayashi Miho , Higashiyama Hiroyuki , Yamamoto Yukio , Fuyuhiro Haruko , Komure Osamu , Tanaka Fumiaki , Sobue Gen , Tsuchiya Kuniaki , Hamada Koji , Sasaki Hidenao , Takeda Kohsuke , Ichijo Hidenori , Kakizuka Akira
Published: March 2003

Background

A novel class of inherited human neurodegenerations is now known to be caused by expanded CAG repeats encoding polyglutamines. Polyglutamine‐containing protein fragments have been shown to accumulate as aggregates in the nucleus and in the cytoplasm, and to induce cell death when expressed in cultured cells, leading to the proposal that polyglutamine aggregation is an important step in the pathogenesis. Supporting this, nuclear inclusions containing expanded polyglutamines have been identified in neurones from the brains of patients and in neurones from transgenic mouse models of this class of neural disorders.

Results

We analysed the consequences of polyglutamine expression in PC12 neuronal cells. Activated SEK1 accumulated with nuclear but not cytoplasmic polyglutamine aggregations, which consequently triggers cell death. Cell death induced by polyglutamine expression was inhibited by a dominant‐negative SEK1 (DN‐SEK1), but not by DN‐SEK1 tagged with a nuclear export signal. Steady state SEK1 expression itself was enhanced two to three‐fold. Nuclearly aggregated polyglutamines, which were identified in PML bodies, co‐localized with not only activated SEK1 but also activated c‐Jun. We also observed that nuclear inclusion‐positive neurones from brains with Huntington's disease expressed SEK1.

Conclusions

This study provides molecular links between the neurodegeneration observed in polyglutamine diseases, cell death signalling kinase cascades and nuclear subdomains related to cell death. We propose that the nuclear PML bodies containing polyglutamine aggregates activate the SEK1‐JNK kinase cascade, resulting in the transduction of a death signal.
Central role for Cdc45 in establishing an initiation complex of DNA replication in Xenopus egg extracts
Authors: Mimura Satoru , Masuda Taro , Matsui Tomoko , Takisawa Haruhiko
Published: March 2003

Background

In eukaryotes, chromosomal DNA is licensed to be replicated through the sequential loading of the origin recognition complex, Cdc6 and mini‐chromosome maintenance protein complex (MCM) onto chromatin. However, how the replication machinery is assembled onto the licensed chromatin during initiation of replication is poorly understood.

Results

Using Xenopus egg extracts, we have investigated the role of Cdc45 in the loading of various replication proteins onto chromatin at the onset of S phase, and found that Cdc45, which required MCM for its loading, was essential for the sequential loading of replication protein A (RPA), DNA polymerase α and proliferating cell nuclear antigen (PCNA) onto chromatin. The assembly of DNA polymerase ɛ onto chromatin required Cdc45 but did not require DNA polymerase α. Analysis of nuclease‐digested chromatin fractions shows that Cdc45 formed a stable complex with either MCM or DNA polymerase α on chromatin.

Conclusions

These results demonstrate a central role for Cdc45 in activation of the licensed chromatin to form replication complexes at the onset of S phase, and suggest that Cdc45 has a dual role in the initiation of DNA replication: the unwinding of DNA and the recruiting of DNA polymerases onto DNA.
Nucleocytoplasmic protein traffic and its significance to cell function
Authors: Yoneda Yoshihiro
Published: March 2003

In eukaryotic cells, cell functions are maintained in an orderly manner through the continuous traffic of various proteins between the cell nucleus and the cytoplasm. The nuclear import and export of proteins occurs through nuclear pore complexes and typically requires specific signals: the nuclear localization signal and nuclear export signal, respectively. The transport pathways have been found to be highly divergent, but are known to be largely mediated by importin β‐like transport receptor family molecules. These receptor molecules bind to and carry their cargoes directly or via adapter molecules. A small GTPase Ran ensures the directionality of nuclear transport by regulating the interaction between the receptors and their cargoes through its GTP/GDP cycle. Moreover, it has been recently elucidated how the transport system is involved in various functions of cell physiology, such as cell cycle control.
BIP, a BRAM‐interacting protein involved in TGF‐β signalling, regulates body length in Caenorhabditis elegans
Authors: Sugawara Katsura , Morita Kiyokazu , Ueno Naoto , Shibuya Hiroshi
Published: March 2003

Background The TGF‐β superfamily has diverse biological activities and is involved in the early development of animals. We previously identified a novel family member, BMP receptor associated molecule (BRAM), which binds to the intracellular domain of BMP type IA receptor and is involved in the BMP signalling pathway.

Results To identify novel molecules involved in TGF‐β signalling pathways, we performed yeast two‐hybrid screening using BRAM as bait. From a Xenopus cDNA library, we cloned a cDNA encoding 693 amino acids and containing the motif for an oxysterol binding protein (OSBP), which we designated BRAM interacting protein (BIP). We then isolated a BIP homologue from the Caenorhabditis elegans that encodes 733 amino acids and also contains the OSBP‐like motif. Immunoprecipitation and Western blotting studies revealed that C. elegans BIP could interact with the C. elegans BRAM homologues BRA‐1 and BRA‐2. C. elegans BIP was expressed in pharyngeal muscle, hypodermis and several neuronal cells, an expression pattern overlaps with those of BRA‐1 and BRA‐2. Finally, we found that inhibition of BIP expression in C. elegans by double stranded RNA interference produces a Sma phenotype.

Conclusions BIP was isolated using the yeast two‐hybrid systems. BIP may function in the TGF‐β pathway and regulate body length in C. elegans.
Functional interactions of an archaeal sliding clamp with mammalian clamp loader and DNA polymerase δ
Authors: Ishino Yoshizumi , Tsurimoto Toshiki , Ishino Sonoko , Cann Isaac K. O.
Published: March 2003

BackgroundBy the total genome sequencing of several archaeal organisms, it has been confirmed that many archaeal proteins related to genetic information systems, including DNA replication, transcription and translation, have similar sequences to those of eukaryotes. In eukaryotic DNA replication, proliferating cell nuclear antigen (PCNA) works in clamping DNA polymerases on the DNA template and accomplishes a processive DNA synthesis. Archaea encode PCNA homologues in their genomes andPyrococcus furiosusPCNA (PfuPCNA) stimulates the DNA synthesizing activities of the DNA polymerases, Pol I and Pol II, in this organism.

ResultsWe have demonstrated thatPfuPCNA interacts functionally with calf thymus DNA polymerase δ (Pol δ) and stimulates its activity. Moreover, human replication factor C (RFC) enhances thePfuPCNA‐dependent DNA synthesis activity of Pol δ, indicating that human RFC works as the clamp loader forPfuPCNA. These results showed that the three‐dimensional structures of archaral PCNA and RFC are actually similar enough to their eukaryotic counterparts to allow a molecular substitution between the two biological domains, albeit at a lower efficiency.

ConclusionsWe found that the archaeal molecule interacts functionally with the eukaryotic members in the DNA replication process. This finding supports the idea that studies on the DNA replication mechanism of archaeal organisms will provide many important clues for understanding of the intricate molecular recognition that is inherent to the DNA replication machinery in Eukarya.
Two domains of Nrf2 cooperatively bind CBP, a CREB binding protein, and synergistically activate transcription
Authors: Katoh Yasutake , Itoh Ken , Yoshida Eisaku , Miyagishi Makoto , Fukamizu Akiyoshi , Yamamoto Masayuki
Published: March 2003

Background Nrf2 belongs to the Cap‐N‐Collar (CNC) transcription factor family and is essential for the antioxidant responsive element (ARE)‐mediated expression of a group of detoxifying and antioxidant genes. The forced expression of Nrf2 in mammalian cells activates the expression of target genes through the ARE, with Nrf2 showing the highest transactivation activity among the CNC family of transcription factors. To elucidate the molecular mechanisms generating this potent transactivation activity, we examined the functions of the domains within Nrf2.

Result We found that Nrf2 contains two transcription activation domains, Neh4 and Neh5, which act synergistically to attain maximum a activation of reporter gene expression. Neh4 and Neh5 both individually and cooperatively bind to CBP (CREB (cAMP Responsive Element Binding protein) Binding Protein). In fact, the specific inhibitor of CBP, adenovirus E1A protein, significantly reduced Nrf2 activity. Importantly, the CBP‐binding activity of Nrf2 deletion mutants positively correlated with their transactivation activity. Neh5 contains a motif which is commonly conserved among the CNC factors, whereas Neh4 contains the novel CBP‐interacting motif recently identified in p53 and E2F.

Conclusions Our results indicate that Nrf2 exploits the cooperative binding of two independent transactivation domains to CBP in the acquisition of a potent transactivation activity.
Disruption of MSSP, c‐myc single‐strand binding protein, leads to embryonic lethality in some homozygous mice
Authors: Fujimoto Mitsuaki , Matsumoto Ken‐ichi , Iguchi‐Ariga Sanae M. M. , Ariga Hiroyoshi
Published: March 2003

Background MSSP, c‐myc single‐strand binding protein, works as a factor for DNA replication, transcription, apoptosis induction, and myc/ras cooperative transformation. The cDNAs encoding four of the family proteins, MSSP‐1, MSSP‐2, Scr2 and Scr3, were cloned. These proteins possess two copies of putative RNA binding domains, RNP‐A and RNP‐B, and these RNA binding domains have been suggested to be indispensable to the functions of MSSP.

Results To elucidate its role in vivo, we generated Mssp knockout mice by homologous recombination in embryonic stem cells. Although intercrossing of Mssp+/– mice gave rise to mice homozygous to the mutant Mssp allele (Mssp−/–) and the Mssp−/– mice, once born, did not display an overt phenotype, the ratio of littermates born among Mssp+/+, Mssp+/– and Mssp−/– mice was 1 : 1.6 : 0.5, which is not a typical Mendelian ratio. When E2.5 embryos from the pregnant mice were cultured in vitro for 5 days, the inner cell mass and trophoblast giant cells in wild‐type (Mssp+/+) E2.5 embryos developed normally. However, Mssp−/– E2.5 embryos displayed significant defects in growth and development. Since Mssp was expressed in uterine gland‐transported glycogen, we evaluated the hormonal state of wild‐type and Mssp−/– mice. The progesterone concentration of Mssp−/– mice was decrease to 6.5% of that of wild‐type mice at E2.5.

Conclusions These results suggest that the deletion of the mssp gene results in both the growth defect in the embryo and the hormonal defect in adult female mouse. The embryonic defect and a decreased concentration of progesterone in female mice reflect a development defect of the pre‐implantation embryo in Mssp−/– mice, thereby leading to embryonic lethality.
Vacuolar membrane dynamics revealed by GFP‐AtVam3 fusion protein
Authors: Uemura Tomohiro , Yoshimura Shige H. , Takeyasu Kunio , Sato Masa H.
Published: March 2003

Background: The plant vacuole is a multifunctional organelle that has various physiological functions. The vacuole dynamically changes its function and shape, dependent on developmental and physiological conditions. Our current understanding of the dynamic processes of vacuolar morphogenesis has suffered from the lack of a marker for observing these processes in living cells.

Results: We have developed transgenic Arabidopsis thaliana expressing a vacuolar syntaxin‐related molecule (AtVam3/SYP22) fused with green fluorescent protein (GFP). Observations using confocal laser scanning microscopy demonstrated that the plant vacuole contained a dynamic membrane system that underwent a complex architectural remodelling. Three‐dimensional reconstitution and time‐lapse analysis of GFP‐fluorescence images revealed that cylindrical and sheet‐like structures were present in the vacuolar lumen and were moving dynamically. The movement, but not the structure itself, was abolished by cytochalasin D, an inhibitor of actin polymerization. This moving structure, which sometimes penetrated through the vacuolar lumen, possessed a dynamic membrane architecture similar to the previously recognized ‘transvacuolar strand.’

Conclusion: We propose two possible models for the formation of the vacuolar lumenal structure. Membrane structures including protruding tubules and reticular networks have recently been recognized in many other organelles, and may be actively involved in intra‐ and/or inter‐organelle signalling.
Further understanding of the β‐globin locus regulation at the molecular level: looping or linking models?
Authors: Tang Yi , Liu De‐pei , Liang Chih‐Chuan
Published: March 2003

The human β‐globin locus is a classic model of the eukaryotic multigene family with tissue‐ and temporally specific expression. Over the past few years, great advances have been achieved in studies of β‐globin locus regulation. The dominant role of the β‐globin locus control region (LCR) in chromatin opening and developmental switching has been challenged, and elements beyond the LCR have been studied in depth. More recently, the fields of research have been expanded to intergenic transcription, nuclear localization and histone modification. Several models have been proposed to elucidate the regulation mechanism; among them, the looping and linking models are the most prevalent. Different models are the summarization of the observations made at different times and a persuasive model must be based on a systematic understanding of the numerous observations. The objective of this review is to provide an overview of progress in the area of β‐globin regulation and then to discuss models for it.
A possible linkage between AMP‐activated protein kinase (AMPK) and mammalian target of rapamycin (mTOR) signalling pathway
Authors: Kimura Naoki , Tokunaga Chiharu , Dalal Sushila , Richardson Christine , Yoshino Ken‐ichi , Hara Kenta , Kemp Bruce E. , Witters Lee A. , Mimura Osamu , Yonezawa Kazuyoshi
Published: March 2003

Background: The mammalian target of rapamycin (mTOR) regulates multiple cellular functions including translation in response to nutrients, especially amino acids. AMP‐activated protein kinase (AMPK) modulates metabolism in response to energy demand by responding to changes in AMP.

Results: The treatment of SV40‐immortalized human corneal epithelial cells (HCE‐T cells) with 5‐aminoimidazole‐4‐carboxamide ribonucleoside (AICAR), widely used as an AMPK activator, inhibits p70 S6k activities. Altered glucose availability, which regulates AMPK activity, also modulates the activity of p70 S6k. AICAR treatment also inhibits phosphorylation of Thr‐412 in the p70 S6 kinase (p70 S6k), which is indispensable for the activity. Furthermore, over‐expression of mutant AMPK subunits by stable expression in rabbit pulmonary fibroblast cell lines (PS120 cells) also modulates p70 S6k activity. The insensitivity of the rapamycin‐resistant p70 S6k variant to AICAR treatment suggests that the inhibition of p70 S6k is mediated through a common effector, supporting a model whereby mTOR and its downstream effector are controlled by AMPK.

Conclusion: These results indicate that the AMPK and mTOR signalling pathways are possibly linked. In addition to the mTOR signal acting as a priming switch that modulates p70 S6k activation, AMPK appears to provide an overriding switch linking p70 S6k regulation to cellular energy metabolism.
Efficient finite‐difference modelling of seismic waves using locally adjustable time steps
Authors: Falk Joachim , Tessmer Ekkehart , Gajewski Dirk
Published: March 2003

Conventional finite‐difference modelling algorithms for seismic forward modelling are based on a time‐stepping scheme with a constant (global) time step. Large contrasts in the velocity model or in the spatial sampling rate cause oversampling in time for some regions of the model. The use of locally adjustable time steps can save large amounts of computation time for certain modelling configurations.  The computation of spatial derivatives across the transition zone between regions of the model with different temporal sampling requires the definition of the wavefield at corresponding time levels on both sides of the transition zone. This condition can be obtained by extrapolation in time, which is inaccurate, or by multiple time integration in the transition zone. The error in the latter solution is of the same order as the conventional time‐stepping scheme because both methods are based on the same iteration formula. The technique of multiple time integration simply requires the use of different sizes of time step. It is applicable only for certain factors of variation of the time step.
Seismic imaging of the shallow subsurface: shear‐wave case histories
Authors: Dasios  , McCann  , Astin  , McCann  , Fenning
Published: March 2003

Obtaining high‐resolution images of the geology and hydrogeology of the subsurface in the depth range from ground level to 50 m is one of the major challenges of modern geophysics. The methods which are commonly used (such as compressional‐wave surveys and ground‐penetrating radar) often suffer from adverse effects caused by the near‐surface conditions, changes in water saturation and various sources of noise. This paper demonstrates some of the advantages offered by the use of shear‐wave seismology and by the combination of shear‐ and compressional‐wave seismic methods in shallow subsurface investigations.

Multicomponent shallow seismic tests were carried out at four different sites to examine the effectiveness of different acquisition geometries under a variety of near‐surface geological conditions. Near‐surface conditions encountered at the sites included thick clays, clay/sand sequences overlying Chalk, mudstone overlying granodiorite bedrock and landfill material.

Under all conditions, shear‐wave data acquisition was found to have advantages over compressional‐wave acquisition for the investigation of the shallow subsurface. Shear head waves, being unaffected by water saturation, achieved penetration to greater depths at a site in Crewkerne, Dorset where compressional head‐wave penetration was limited to the near‐surface layers. Better vertical resolution was achieved at shallow depths using shear‐wave reflection energy at a landfill site. Shear‐wave reflections from shallow interfaces were in some cases less affected by noise compared with the equivalent compressional‐wave reflections. Combinations of shear‐ and compressional‐wave data recording allowed the measurement of a Poisson's ratio log and gave indications of seismic anisotropy at two sites where dipping clay layers were present.
Gravity probability tomography: a new tool for buried mass distribution imaging
Authors: Mauriello Paolo , Patella Domenico
Published: March 2003

Following the probability tomography principles previously introduced to image the sources of electric and electromagnetic anomalies, we demonstrate that a similar approach can be used to analyse gravity data. First, we give a coherent derivation of the Bouguer anomaly concept as a Newtonian‐type integral for an arbitrary mass distribution buried below a non‐flat topography. A discretized solution of this integral is then derived as a sum of elementary contributions, which are cross‐correlated with the gravity data function in the expression for the total power associated with the Bouguer anomaly. To image the mass distribution underground we introduce a mass contrast occurrence probability function using the cross‐correlation product of the observed Bouguer anomaly and the synthetic field due to an elementary mass contrast source. The tomographic procedure consists of scanning the subsurface with the elementary source and calculating the occurrence probability function at the nodes of a regular grid. The complete set of grid values is used to highlight the zones of highest probability of mass contrast concentrations. Some synthetic and field examples demonstrate the reliability and resolution of the new gravity tomographic approach.
Depth migration of shot records in heterogeneous, transversely isotropic media using optimum explicit operators
Authors: Zhang Jianfeng , Verschuur D.J. , Wapenaar C.P.A.
Published: March 2003

A space–frequency domain 2D depth‐migration scheme is generalized for imaging in the presence of anisotropy. The anisotropy model used is that of a transversely isotropic (TI) medium with a symmetry axis that can be either vertical or tilted. In the proposed scheme the anisotropy is described in terms of Thomsen parameters; however, the scheme can accommodate a wide range of anisotropy rather than only weak anisotropy. Short spatial convolution operators are used to extrapolate the wavefields recursively in the space–frequency domain for both qP‐ and qSV‐waves. The weighted least‐squares method for designing isotropic optimum operators is extended to asymmetric optimum explicit extrapolation operators in the presence of TI media with a tilted symmetry axis. Additionally, an efficient weighted quadratic‐programming design method is developed. The short spatial length of the derived operators makes it possible for the proposed scheme to handle lateral inhomogeneities. The performance of the operators, designed by combining the weighted least‐squares and weighted quadratic‐programming methods, is demonstrated by migration impulse responses of qP and qSV propagation modes for the weak and strong TI models with both vertical and tilted symmetry axes. Finally, a table‐driven shot‐record depth‐migration scheme is proposed, which is illustrated for finite‐difference modelled shot records in TI media.
Improved amplitude preservation for prestack depth migration by inverse scattering theory
Authors: Shin Changsoo , Jang Seonghyung , Min Dong‐Joo
Published: March 2003

A prestack reverse time‐migration image is not properly scaled with increasing depth. The main reason for the image being unscaled is the geometric spreading of the wavefield arising during the back‐propagation of the measured data and the generation of the forward‐modelled wavefields. This unscaled image can be enhanced by multiplying the inverse of the approximate Hessian appearing in the Gauss–Newton optimization technique. However, since the approximate Hessian is usually too expensive to compute for the general geological model, it can be used only for the simple background velocity model.We show that the pseudo‐Hessian matrix can be used as a substitute for the approximate Hessian to enhance the faint images appearing at a later time in the 2D prestack reverse time‐migration sections. We can construct the pseudo‐Hessian matrix using the forward‐modelled wavefields (which are used as virtual sources in the reverse time migration), by exploiting the uncorrelated structure of the forward‐modelled wavefields and the impulse response function for the estimated diagonal of the approximate Hessian. Although it is also impossible to calculate directly the inverse of the pseudo‐Hessian, when using the reciprocal of the pseudo‐Hessian we can easily obtain the inverse of the pseudo‐Hessian. As examples supporting our assertion, we present the results obtained by applying our method to 2D synthetic and real data collected on the Korean continental shelf.
Imaging magnetic sources using Euler's equation
Authors: Hsu Shu‐Kun
Published: March 2003

The conventional Euler deconvolution method has the advantage of being independent of magnetization parameters in locating magnetic sources and estimating their corresponding depths. However, this method has the disadvantage that a suitable structural index must be chosen, which may cause spatial diffusion of the Euler solutions and bias in the estimation of depths to the magnetic sources. This problem becomes more serious when interfering anomalies exist. The interpretation of the Euler depth solutions is effectively related to the model adopted, and different models may have different structural indices. Therefore, I suggest a combined inversion for the structural index and the source location from the Euler deconvolution, by using only the derivatives of the magnetic anomalies. This approach considerably reduces the diffusion problem of the location and depth solutions. Consequently, by averaging the clustered solutions satisfying a given criterion for the solutions, we can image the depths and attributes (or types) of the causative magnetic sources. Magnetic anomalies acquired offshore northern Taiwan are used to test the applicability of the proposed method.
Effects of pore aspect ratios on velocity prediction from well‐log data
Authors: Yan Jun , Li Xiang‐Yang , Enru Liu
Published: March 2003

We develop a semi‐empirical model which combines the theoretical model of Xu and White and the empirical formula of Han, Nur and Morgan in sand–clay environments. This new model may be used for petrophysical interpretation of P‐ and S‐wave velocities. In particular, we are able to obtain an independent estimation of aspect ratios based on log data and seismic velocity, and also the relationship between velocities and other reservoir parameters (e.g. porosity and clay content), thus providing a prediction of shear‐wave velocity. To achieve this, we first use Kuster and Toksöz's theory to derive bulk and shear moduli in a sand–clay mixture. Secondly, Xu and White's model is combined with an artificial neural network to invert the depth‐dependent variation of pore aspect ratios. Finally these aspect ratio results are linked to the empirical formula of Han, Nur and Morgan, using a multiple regression algorithm for petrophysical interpretation. Tests on field data from a North Sea reservoir show that this semi‐empirical model provides simple but satisfactory results for the prediction of shear‐wave velocities and the estimation of reservoir parameters.
Carbon cycling in cultivated land and its global significance
Authors: Buyanovsky Gregory A. , Wagner George H.
Published: March 2003

Long‐term data from Sanborn Field, one of the oldest experimental fields in the USA, were used to determine the direction of soil organic carbon (SOC) dynamics in cultivated land. Changes in agriculture in the last 50 years including introduction of more productive varieties, wide scale use of mineral fertilizers and reduced tillage caused increases in total net annual production (TNAP), yields and SOC content. TNAP of winter wheat more than doubled during the last century, rising from 2.0–2.5 to 5–6 Mg ha–1 of carbon, TNAP of corn rose from 3–4 to 9.5–11.0 Mg ha–1 of carbon. Amounts of carbon returned annually with crop residues increased even more drastically, from less than 1 Mg ha–1 in the beginning of the century to 3–3.5 Mg ha–1 for wheat and 5–6 Mg ha–1 for corn in the 90s. These amounts increased in a higher proportion because in the early 50s removal of postharvest residues from the field was discontinued. SOC during the first half of the century, when carbon input was low, was mineralized at a high rate: 89 and 114 g m–2 y–1 under untreated wheat and corn, respectively. Application of manure decreased losses by half, but still the SOC balance remained negative. Since 1950, the direction of the carbon dynamics has reversed: soil under wheat monocrop (with mineral fertilizer) accumulated carbon at a rate about 50 g m–2 y–1, three year rotation (corn/wheat/clover) with manure and nitrogen applications sequestered 150 g m2 y–1 of carbon. Applying conservative estimates of carbon sequestration documented on Sanborn Field to the wheat and corn production area in the USA, suggests that carbon losses to the atmosphere from these soils were decreased by at least 32 Tg annually during the last 40–50 years. Our computations prove that cultivated soils under proper management exercise a positive influence in the current imbalance in the global carbon budget.
A free‐air enrichment system for exposing tall forest vegetation to elevated atmospheric CO2
Authors: Hendrey George R. , Ellsworth David S. , Lewin Keith F. , Nagy JohN.
Published: March 2003

A free‐air CO2 enrichment (FACE) system was designed to permit the experimental exposure of tall vegetation such as stands of forest trees to elevated atmospheric CO2 concentrations ([CO2]a) without enclosures that alter tree microenvironment. We describe a prototype FACE system currently in operation in forest plots in a maturing loblolly pine (Pinus taeda L.) stand in North Carolina, USA. The system uses feedback control technology to control [CO2] in a 26 m diameter forest plot that is over 10 m tall, while monitoring the 3D plot volume to characterize the whole‐stand CO2 regime achieved during enrichment. In the second summer season of operation of the FACE system, atmospheric CO2 enrichment was conducted in the forest during all daylight hours for 96.7% of the scheduled running time from 23 May to 14 October with a preset target [CO2] of 550 μmol mol–1, ≈ 200 μmol mol–1 above ambient [CO2]. The system provided spatial and temporal control of [CO2] similar to that reported for open‐top chambers over trees, but without enclosing the vegetation. The daily average daytime [CO2] within the upper forest canopy at the centre of the FACE plot was 552 ± 9 μmol mol–1 (mean ± SD). The FACE system maintained 1‐minute average [CO2] to within ± 110 μmol mol–1 of the target [CO2] for 92% of the operating time. Deviations of [CO2] outside of this range were short‐lived (most lasting < 60 s) and rare, with fewer than 4 excursion events of a minute or longer per day. Acceptable spatial control of [CO2] by the system was achieved, with over 90% of the entire canopy volume within ± 10% of the target [CO2] over the exposure season. CO2 consumption by the FACE system was much higher than for open‐top chambers on an absolute basis, but similar to that of open‐top chambers and branch bag chambers on a per unit volume basis. CO2 consumption by the FACE system was strongly related to windspeed, averaging 50 g CO2 m–3 h–1 for the stand for an average windspeed of 1.5 m s–1 during summer. The [CO2] control results show that the free‐air approach is a tractable way to study long‐term and short‐term alterations in trace gases, even within entire tall forest ecosystems. The FACE approach permits the study of a wide range of forest stand and ecosystem processes under manipulated [CO2]a that were previously impossible or intractable to study in true forest ecosystems.
Do open‐top chambers overestimate the effects of rising CO2 on plants? An analysis using spring wheat
Authors: Van Oijen M. , Schapendonk A. H. C. M. , Jansen M. J. H. , Pot C. S. , Maciorowski R.
Published: March 2003

The microclimate in facilities for studying effects of elevated CO2 on crops differs from ambient conditions. Open‐top chambers (OTCs) increase temperature by 1–3 °C. If temperature and CO2 interact in their effect on crops, this would limit the value of OTC experiments. Furthermore, interaction of CO2 and temperature deserves study because increases in atmospheric CO2 concentration are expected to cause global warming.

This paper describes two experiments in which a recently developed cooling system for OTCs was used to analyse the effects of temperature on photosynthesis, growth and yield of spring wheat (Triticum aestivum L., cv. Minaret). Two levels of CO2 were used (350 and 700 ppm), and two levels of temperature, with cooled OTCs being 1.6–2.4 °C colder than noncooled OTCs.

Photosynthetic rates were increased by elevated CO2, but no effect of temperature was found. Cross‐switching CO2 concentrations as well as determination of A–Ci curves showed that plant photosynthetic capacity after anthesis acclimated to elevated CO2. The acclimation may be related to the effects of CO2 on tissue composition: elevated CO2 decreased leaf nitrogen concentrations and increased sugar content. Calculations of the seasonal mean crop light‐use efficiency (LUE) were consistent with the photosynthesis data in that CO2 increased LUE by 20% on average whereas temperature had no effect. Both elevating CO2 and cooling increased grain yield, by an average of 11% and 23%, respectively. CO2 and temperature stimulated yield via different mechanisms: CO2 increased photosynthetic rate, but decreased crop light interception capacity (LAI), whereas cooling increased grain yield by increasing LAI and extending the growing season with 10 days. The effects of CO2 and temperature were not additive: the CO2 effect was about doubled in the noncooled open‐top chambers. In most cases, effects on yield were mediated through increased grain density rather than increased individual grain weights.

The higher growth response to elevated CO2 in noncooled vs. cooled OTCs shows that a cooling system may remove a bias towards overestimating crop growth response to CO2 in open‐top chambers.
Carbon balance of a boreal patterned peatland
Authors: Waddington J. M. , Roulet N. T.
Published: March 2003

Measurements of the spatial variability of methane (CH4) emissions, net CO2 ecosystem exchange (NEE), and dissolved carbon (CH4, CO2, and DOC) were made in a boreal patterned peatland in northern Sweden in the summers (May to September) of 1992 and 1993. Carbon balance terms were measured and the carbon balance inferred at different peatland surface topography features (e.g. ridges, lawns, and pools) and at different positions within the peatland (e.g. plateau, margin). Combining these data permits a comparison of the carbon balance at the peatland scale for the two field seasons.

Trends in the spatial variability of the net carbon storage, as determined by the difference between inputs and outputs, suggest that carbon storage decreased in lawns from the margin of the peatland to the central plateau, while the reverse trend occurred in ridges. This indicates a difference in carbon exchange processes between sites with different surface topography due to differences in soil moisture and temperature.

Total carbon storage for the peatland, weighted for topographic variability, indicates that the peatland gained carbon in 1992 (2.0 g C m− 2), but lost carbon in 1993 ( −  7.6 g C m− 2). There was little variation in mean seasonal air temperature and total precipitation between the two years suggesting that the timing and magnitude of temperature and precipitation variation within the growing season are important for the season carbon balance. Because the carbon storage differences were small relative to the potential errors we conclude that the peatland was neither a net sink nor source of atmospheric carbon. This research demonstrates the importance of position in a peatland for the inference of long‐term carbon accumulation and the assessment of contemporary exchange rates.
A new global 1‐km dataset of percentage tree cover derived from remote sensing
Authors: Defries R. S. , Hansen M. C. , Townshend J. R. G. , Janetos A. C. , Loveland T. R.
Published: March 2003

Accurate assessment of the spatial extent of forest cover is a crucial requirement for quantifying the sources and sinks of carbon from the terrestrial biosphere. In the more immediate context of the United Nations Framework Convention on Climate Change, implementation of the Kyoto Protocol calls for estimates of carbon stocks for a baseline year as well as for subsequent years. Data sources from country level statistics and other ground‐based information are based on varying definitions of ‘forest’ and are consequently problematic for obtaining spatially and temporally consistent carbon stock estimates. By combining two datasets previously derived from the Advanced Very High Resolution Radiometer (AVHRR) at 1 km spatial resolution, we have generated a prototype global map depicting percentage tree cover and associated proportions of trees with different leaf longevity (evergreen and deciduous) and leaf type (broadleaf and needleleaf). The product is intended for use in terrestrial carbon cycle models, in conjunction with other spatial datasets such as climate and soil type, to obtain more consistent and reliable estimates of carbon stocks. The percentage tree cover dataset is available through the Global Land Cover Facility at the University of Maryland at http://glcf.umiacs.umd.edu.