bluuebunny/crossref_metadata_2025 huggingface dataset:
Close kinship of human 20α‐hydroxysteroid dehydrogenase gene with three aldo‐keto reductase genes
Authors: Nishizawa Mikio , Nakajima Tatsuya , Yasuda Katsuhiko , Kanzaki Hideharu , Sasaguri Yasuyuki , Watanabe Kikuko , Ito Seiji
Published: March 2003

Background

20α‐Hydroxysteroid dehydrogenase (HSD) is a member of the aldo‐keto reductase (AKR) superfamily and catalyses the reaction of progesterone to the inactive form 20α‐hydroxyprogesterone. Progesterone plays an important role in the maintenance of pregnancy, and, in rodents, plasma progesterone levels decrease abruptly just before parturition. The induction of 20α‐HSD is thought to be responsible for the decrease in plasma progesterone at term. High homology between human 20α‐HSD [AKR 1C1] cDNA with other AKRs had caused difficulty in gene isolation and expression analysis. Thus, the metabolism of progesterone in the human reproductive system remained unclear.

Results

By hybridization with rat 20α‐HSD [AKR 1C8] cDNA and high‐stringency polymerase chain reaction (PCR) with gene‐specific primers, we were able to isolate the human 20α‐HSD, bile acid‐binding protein (BABP) [AKR 1C2], prostaglandin F synthase (PGFS) [AKR 1C3], and dihydrodiol dehydrogenase (DD) 4 [AKR 1C4] genes. These genes had similar exon‐intron organizations and shared a high homology. The four recombinant enzymes encoded by these genes showed distinct substrate specificity. By reverse transcription‐PCR analysis, human 20α‐HSD, BABP and PGFS mRNAs were expressed ubiquitously, while DD4 mRNA was restricted to the liver. Promoter activities of the 20α‐HSD, BABP and PGFS genes were high, both in ovarian granulosa cells and hepatocytes. Radiation hybridization analysis revealed that all these genes were located close together in chromosome 10.

Conclusion

The human gene encoding for the progesterone‐metabolizing enzyme 20α‐HSD in the female reproductive system was cloned, and its expression and gene localization were elucidated. BABP, PGFS and DD4 genes, which were highly homologous to the 20α‐HSD gene, were also cloned, and their structure and function were characterized.
Intronic U50 small‐nucleolar‐RNA (snoRNA) host gene of no protein‐coding potential is mapped at the chromosome breakpoint t(3;6)(q27;q15) of human B‐cell lymphoma
Authors: Tanaka Ritsuko , Satoh Hitoshi , Moriyama Masatsugu , Satoh Kasumi , Morishita Yasuyuki , Yoshida Syouko , Watanabe Toshiki , Nakamura Yoshikazu , Mori Shigeo
Published: March 2003

Background

In eukaryotic cells, nucleolar processing of preribosomal RNAs (prerRNAs) is assisted by a large number of small nucleolar RNAs (snoRNAs) that function in the 2′‐O‐methylation or the pseudouridylation of rRNAs. Most snoRNAs so far characterized are encoded and processed from introns of premRNAs.

Results

We found a novel intronic snoRNA gene, named U50HG, located on chromosome 6q15, at the breakpoint of chromosomal translocation t(3;6)(q27;q15). The U50HG gene is composed of six exons, whose spliced transcripts have little potential for coding a protein, and its introns produce both U50 and U50‐like (U50′) snoRNAs that are localized in nucleoli. It possesses an oligopyrimidine tract that is characteristic of the 5′‐terminal oligopyrimidine (5′TOP) class of genes which have been shown to be coordinately regulated in response to cell growth.

Conclusions

U50HG is a member of the nonprotein‐coding multiple snoRNA host gene family, as well as of the 5′TOP gene family similar to UHG (U22 host gene), U17HG (U17 host gene), U19HG (U19 host gene) and gas5 (growth arrest‐specific transcript 5 gene). It is novel to find that the snoRNA gene is located at the breakpoint of chromosomal translocation t(3;6)(q27;q15) involved in human B‐cell lymphoma.
Rev‐dependent association of the intron‐containing HIV‐1 gag mRNA with the nuclear actin bundles and the inhibition of its nucleocytoplasmic transport by latrunculin‐B
Authors: Kimura Tominori , Hashimoto Iwao , Yamamoto Akitsugu , Nishikawa Masao , Fujisawa Jun‐ichi
Published: March 2003

Background

A hallmark of HIV‐1 gene expression is that unspliced genomic RNA, which also acts as mRNA for the expression of Gag/Pol, is exported to the cytoplasm. Rev directs this transport through the nuclear export signal (NES).

Results

Fluorescence in situ hybridization and immunocytochemistry demonstrated that gag mRNA, Rev, and its NES receptor, CRM1, and RanGTPase formed nuclear tracks which were congruent with underlying β‐actin bundles. Actin bundle formation was confirmed electron‐microscopically. These bundles were observed upon Rev‐containing gag RNP formation. The loss of bundles was associated with the nuclear retention of gag mRNA. Reverse transcription‐polymerase chain reaction analysis of both cytoplasmic and nuclear gag mRNAs demonstrated that disruption of nuclear actin filament formation by latrunculin‐B (LAT‐B), an F‐actin depolymerizing compound, resulted in the dose‐dependent inhibition of gag mRNA export. The differential subtyping of the mRNA‐positive cells confirmed morphologically the effect of LAT‐B treatment. The export inhibition was specific to gag mRNA and export of fully spliced HIV‐1 tat/rev mRNAs as well as cellular GAPDH mRNA was not affected by the compound.

Conclusions

Nuclear β‐actin bundles are suggested to be functionally involved in the Rev‐dependent nucleocytoplasmic transport of intron‐containing HIV‐1 gag mRNA.
Regulation of human myocilin/TIGR gene transcription in trabecular meshwork cells and astrocytes: role of upstream stimulatory factor
Authors: Kirstein Lucienne , Cvekl Ales , Chauhan Bharesh K. , Tamm Ernst R.
Published: March 2003

Background

Mutations in the myocilin (MYOC)/TIGR gene are responsible for autosomal‐dominant juvenile primary open‐angle glaucoma (POAG). In patients with non‐autosomal‐dominant POAG, such mutations are rare, but the expression of MYOC/TIGR in the trabecular meshwork (TM) of the eye is considerably higher than in normals. We performed transfection, DNAse I footprinting, mutagenesis and electrophoretic mobility shift assays (EMSA) to identify elements responsible for the basal transcription of MYOC/TIGR in TM cells and astrocytes.

Results

DNAse I footprinting experiments of the human MYOC/TIGR promoter showed a major protected area between nt −106 to −77, which was not conserved in the homologous region of the mouse myoc/tigr promoter. In addition, the TATA‐box was protected, as well as at least three downstream sites, including an AP‐1‐like sequence. Deletion of the −106 to −77 region caused a substantial loss of functional promotor activity in all cell types. Site‐directed mutagenesis and EMSA experiments revealed the presence of two regulatory elements in the −106 to −77 region. Each of these cis‐elements is essential for minimal promoter activity. The 5′‐half of the region contains a sequence with similarities to NF‐κB‐related sites, however, binding of NF‐κB could not be confirmed by EMSA. The 3′‐half contains a canonical E‐box sequence. EMSA experiments showed that the upstream regulatory factor (USF) was binding to the E‐box sequence and that the binding can be supershifted by specific antibodies.

Conclusions

Several DNA‐protein binding elements contribute to a transcription of MYOC/TIGR, and USF is critically required for its basal transcription in trabecular meshwork cells and astrocytes.
The ERK MAP kinase pathway mediates induction of SGK (serum‐ and glucocorticoid‐inducible kinase) by growth factors
Authors: Mizuno Hiroshi , Nishida Eisuke
Published: March 2003

Background

The ERK MAP kinase pathway plays a pivotal role in growth factor‐induced gene expression. However, genes whose expression is induced by the ERK pathway are not fully defined.

Results

We have identified SGK (serum‐ and glucocorticoid‐inducible kinase) as an ERK‐inducible gene by the subtractive screening of Raf‐inducible genes. SGK is known to be similar in primary structure to AKT/PKB, PKC and PKA. Treatment of quiescent NIH‐3T3 cells with FGF, PDGF or TPA, which induced the sustained activation of ERKs, resulted in the strong induction of SGK, whereas treatment with EGF, which induced the transient activation of ERKs, did not induce a strong expression of SGK. The induction of SGK was blocked by pre‐treatment with a specific MEK inhibitor U0126, and expression of constitutively active MEK was able to induce SGK. Treatment with cycloheximide or vanadate prolonged the increased expression of SGK by FGF, concomitant with a more prolonged activation of ERKs.

Conclusion

Growth factor‐induced activation of the ERK MAP kinase pathway is necessary and sufficient for the induction of SGK.
Functional divergence of the TFL1‐like gene family in Arabidopsis revealed by characterization of a novel homologue
Authors: Mimida Naozumi , Goto Koji , Kobayashi Yasushi , Araki Takashi , Ahn Ji Hoon , Weigel Detlef , Murata Minoru , Motoyoshi Fusao , Sakamoto Wataru
Published: March 2003

Background

The TERMINAL FLOWER 1 (TFL1) gene of Arabidopsis plays an important role in regulating flowering time and in maintaining the fate of inflorescence meristem (IM). TFL1 is a homologue of CENTRORADIALIS (CEN) from Antirrhinum, which is only involved in IM maintenance. Recent mutational studies and the genome project revealed that TFL1 belongs to a small gene family in Arabidopsis, in which functional divergence may have occurred among the members.

Results

We found a new member of the TFL1 gene family, which is mapped on chromosome 2 of Arabidopsis. The predicted protein sequence encoded by this gene is more closely related to that of CEN than other Arabidopsis TFL1 homologues (and therefore named ATC for ArabidopsisthalianaCENTRORADIALIS homologue). Transgenic plants constitutively expressing the ATC gene (35S::ATC), in either wild‐type or tfl1 mutant backgrounds, showed a phenotype similar to that observed in transgenic plants constitutively expressing the TFL1 gene. However, in contrast to TFL1, the expression of ATC was only detected in the hypocotyl of young plants, and not in the IM. In addition, an atc loss‐of‐function mutant, isolated by screening a T‐DNA library, showed no phenotypes that were similar to those of tfl1 mutants.

Conclusion

The phenotypes of transgenic plants over‐expressing ATC suggest that the ATC protein can functionally substitute for TFL1. However, the pattern and level of expression and the loss‐of‐function phenotype indicate that ATC does not participate in the regulation of IM identity, but rather has a role that is different from that of TFL1.
The central MHC gene, BAT1, may encode a protein that down‐regulates cytokine production
Authors: Allcock Richard J. N. , Williams James H. , Price Patricia
Published: March 2003

Background

BAT1 belongs to the DEAD‐box family of RNA‐binding proteins and is encoded in the central MHC. To determine whether it affects immune responses and hence diseases influenced by MHC haplotypes, U937, THP1 and Jurkat cells were stably transfected with anti‐sense DNA corresponding to exons 2–5 of BAT1 using a retroviral vector.

Results

Anti‐sense transfectants carried anti‐sense DNA and expressed anti‐sense mRNA. After mitogenic stimulation, they produced higher levels of TNFα, IL‐1 and IL‐6 than equivalent cells carrying the vector alone, suggesting that BAT1 may down‐regulate acute phase cytokine production. Polyclonal antibodies raised against a peptide in exon 8 of BAT1 recognized ≈50 kDa and ≈38 kDa proteins in all cell lines tested, including the anti‐sense transfectants. Expression was localized to the nucleolus in dividing fibroblasts. However the immunochemistry may be confounded by a recently described gene, DDXL, on chromosome 19, which shares a 89% amino acid identity with BAT1. RT‐PCR analyses established that BAT1 and DDXL mRNA are expressed in resting U937, THP1 and Jurkat cells. BAT1 and DDXL are divergent in the exons selected for the anti‐sense study.

Conclusions

BAT1 is a negative regulator of inflammation. Future studies should address how its functions relate to those of DDXL.
Diverse gene expression and function of semaphorins in developing lung: positive and negative regulatory roles of semaphorins in lung branching morphogenesis
Authors: Kagoshima Masako , Ito Takaaki ,   Hitoshi Kitamura and Yoshio Goshima
Published: March 2003

Background Previously, we reported that Sema3A, one of the secreted repulsive axon guidance molecules, CRMP (collapsin response mediator protein)‐2, a putative intracellular signalling molecule for Sema3A and Sema3A receptor neuropilin‐1 are expressed in the developing lung. Sema3A inhibits branching morphogenesis of embryonic lung in organ culture.

Results We examined the gene expression of Sema3A, Sema3C, Sema3F and their receptors, NP‐1, NP‐2 and plexin‐A1 by in situ hybridization. Transcripts of all six genes were detected in mouse lung from embryonic day E11.5 to E17.5, and displayed highly specific spatiotemporal distributions. The distribution of the receptor genes was detected in patterns which were consistent with known receptor usage of the semaphorins. In contrast to Sema3A, we found that the other class 3 semaphorins, Sema3C and Sema3F, stimulated branching morphogenesis. This stimulatory effect of Sema3C or Sema3F was accompanied by a moderate increase in the incorporation of bromodeoxyuridine (BrdU) into DNA in the terminal epithelial cells.

Conclusion The coordinated expression patterns of different semaphorins and their receptors, together with the specific activities affecting branching morphogenesis, suggest that the semaphorins act as both positive and negative regulators of branching morphogenesis in the developing lung.
Ypel1: a novel nuclear protein that induces an epithelial‐like morphology in fibroblasts
Authors: Farlie Peter , Reid Candice , Wilcox Stephen , Peeters Justine , Reed Gullveig , Newgreen Don
Published: March 2003

Background Embryonic development depends on the regulation of cell morphology and behaviour to carry out morphogenesis. One example of this is the development of the face, which is constructed from independent blocks of tissue that must grow in a coordinated way and then fuse to form a continuous tissue.

Results We have isolated a novel gene of unknown function from mouse and quail embryos in a search for genes involved in craniofacial development. Sequence analysis of this gene, known as Ypel1, demonstrates a striking level of amino acid conservation between vertebrates and invertebrates but no significant homology with any other characterized genes. Ypel1 is expressed in the ventral half of early embryos including the branchial arches from which the face derives. Ypel1 localizes to the nucleus, and transfection into fibroblasts induces an epithelial‐like transition, which is accompanied by alterations to the cytoskeleton and cell adhesion machinery. In addition, human YPEL1 localizes to chromosome 22q11.2, a region associated with a number of syndromes involving malformation of the craniofacial complex.

Conclusion These data suggest a role in regulation of cellular morphology and behaviour that is important for development of the craniofacial complex.
Cell death with predominant apoptotic features in Saccharomyces cerevisiae mediated by deletion of the histone chaperone ASF1/CIA1
Authors: Yamaki Mariko , Umehara Takashi , Chimura Takahiko , Horikoshi Masami
Published: March 2003

Background Although no potential homologues of multicellular apoptotic genes (e.g. Bax, Bak, Bcl‐2, caspases and p53) have been identified in a unicellular eukaryote, previous reports contain several implications of the apoptotic behaviour of yeasts (i.e. Saccharomyces cerevisiae and Schizosaccharomyces pombe). Therefore, whether or not yeast undergoes apoptosis has been a topic of some debate. hCCG1, which is the largest subunit of TFIID and a histone acetyltransferase, appears to be involved in the regulation of apoptosis. The factor hCIA interacts with hCCG1 and functions as a histone chaperone in mammalian cells; its homologue in yeast is Asf1p/Cia1p. Therefore, we anticipated that a yeast mutant in Asf1p/Cia1p would be a valuable tool for studying apoptosis in yeast.

Results We established a strain of S. cerevisiae lacking the histone chaperone ASF1/CIA1. This disruptant, asf1/cia1, arrested preferentially at the G2/M‐phase and died. We systematically analysed the phenotype associated with the death of this mutant yeast and identified many changes, such as fragmentation of the nuclei, condensation and fragmentation of chromatin, reduction of the mitochondrial membrane‐potential, dysfunction of the mitochondrial proton pump, and a discernible release of cytochrome c to cytoplasm that resembles those in apoptotic multicellular organisms. Other changes potentially associated with the death in our mutant included a reduction in the vacuolar membrane potential, dysfunction of the vacuolar proton pump, reduction of endocytosis, and the presence of many autophagic bodies. However, these mutant yeast cells also showed cellular enlargement, which is characteristic of necrosis.

Conclusions Cell death in S. cerevisiae occurs with a phenotype that largely resembles apoptosis in multicellular organisms, but that has some features of necrosis. Therefore, we indicate that yeast undergoes a ‘prototypal active cell death’ that retains some characteristics of passive cell death (necrosis). In addition, we think that active cell death is ubiquitously the essential attribute of life. Although such an active cell death system in yeast remains open to confirmation, we speculate that deletion of the histone chaperone Asf1p/Cia1p inhibits the normal assembly/disassembly of nucleosomes in yeast and thereby initiates the active cell death system.
The interaction between σS, the stationary phase σ factor, and the core enzyme of Escherichia coli RNA polymerase
Authors: Colland Frédéric , Fujita Nobuyuki , Ishihama Akira , Kolb Annie
Published: March 2003

Background: The RNA polymerase holoenzyme of Escherichia coli is composed of a core enzyme (subunit structure α2ββ′) associated with one of the σ subunits, required for promoter recognition. Different σ factors compete for core binding. Among the seven σ factors present in E. coli, σ70 controls gene transcription during the exponential phase, whereas σS regulates the transcription of genes in the stationary phase or in response to different stresses. Using labelled σS and σ70, we compared the affinities of both σ factors for core binding and investigated the structural changes in the different subunits involved in the formation of the holoenzymes.

Results: Using native polyacrylamide gel electrophoresis, we demonstrate that σS binds to the core enzyme with fivefold reduced affinity compared to σ70. Using iron chelate protein footprinting, we show that the core enzyme significantly reduces polypeptide backbone solvent accessibility in regions 1.1, 2.5, 3.1 and 3.2 of σS, while increasing the accessibility in region 4.1 of σS. We have also analysed the positioning of σS on the holoenzyme by the proximity‐dependent protein cleavage method using σS derivatives in which FeBABE was tethered to single cysteine residues at nine different positions. Protein cutting patterns are observed on the β and β′ subunits, but not α. Regions 2.5, 3.1 and 3.2 of σS are close to both β and β′ subunits, in agreement with iron chelate protein footprinting data.

Conclusions: A comparison between these results using σS and previous data from σ70 indicates similar contact patterns on the core subunits and similar characteristic changes associated with holoenzyme formation, despite striking differences in the accessibility of regions 4.1 and 4.2.
Identification of a novel transcription factor, ELYS, expressed predominantly in mouse foetal haematopoietic tissues
Authors: Kimura Naoki , Takizawa Makiko , Okita Keisuke , Natori Osamu , Igarashi Katsuhide , Ueno Masaya , Nakashima Kin‐ichi , Nobuhisa Ikuo , Taga Tetsuya
Published: March 2003

Background:  The precise mechanism governing the generation of haematopoietic stem cells still remains to be understood, partly because the molecules required for early haematopoiesis have not fully been identified.

Results:  We have identified a novel gene expressed in embryonic haematopoietic tissues, designated ELYS (for embryonic large molecule derived from yolk sac), which has no significant homology with any other known molecules. Based on the cDNA sequence, mouse ELYS protein is composed of 2243 amino acid residues and contains an AT‐hook DNA‐binding domain, eight nuclear localization signals (NLSs) at the C‐terminal region, three nuclear export signals (NESs) and two WD repeats at the N‐terminal region. ELYS has a potential to shuttle between the cytoplasm and nucleus. When in the nucleus, ELYS is present in the nuclear matrix. Fusions of the yeast GAL4 DNA‐binding domain and various ELYS mutants reveal the presence of transcriptional activation and inhibitory domains. The ELYS gene is predominantly expressed in embryonic haematopoietic tissues, i.e. foetal liver, spleen, and thymus, whereas the expression is down‐regulated in the adult. In the aorta‐gonad‐mesonephros (AGM) region of an 11.5 dpc mouse embryo, ELYS is expressed in the endothelium lining the dorsal aorta. In the adult bone marrow, ELYS is notably expressed in the Lin−/c‐kit+/Sca‐1+ population.

Conclusions:  We have reported the isolation and characterization of a novel molecule, ELYS. ELYS seems to be a nuclear transcription factor associated with both early and mature haematopoietic events.
Role of nectin in organization of tight junctions in epithelial cells
Authors: Fukuhara Atsunori , Irie Kenji , Yamada Akio , Katata Tatsuo , Honda Tomoyuki , Shimizu Kazuya , Nakanishi Hiroyuki , Takai Yoshimi
Published: March 2003

Background In polarized epithelial cells, cell‐cell adhesion forms specialized membrane structures comprised of claudin‐based tight junctions (TJs) and of E‐cadherin‐based adherens junctions (AJs). These structures are aligned from the apical to the basal side of the lateral membrane, but the mechanism of this organization remains unknown. Nectin is a Ca2+ independent immunoglobulin‐like cell‐cell adhesion molecule which localizes at AJs. Nectin is associated with E‐cadherin through their respective cytoplasmic tail‐binding proteins, afadin and catenins, and involved in the formation of AJs in cooperation with E‐cadherin. We show here that nectin is also involved in the formation of TJs.

Results: During the formation of the junctional complex consisting of AJs and TJs in Madin‐Darby canine kidney (MDCK) cells, claudin and occludin accumulated at the apical sites of the nectin‐based cell‐cell adhesion sites. This accumulation of claudin and occludin was inhibited by inhibitors acting on the trans interaction of nectin. The barrier function of TJs was also impaired by the nectin inhibitors. It has been shown that a phorbol ester promotes the formation of a TJ‐like structure in an E‐cadherin‐independent manner. This phorbol ester‐induced formation of the TJ‐like structure was also inhibited by the nectin inhibitors.

Conclusions: These results suggest a role of the nectin‐afadin system in the organization of TJs as well as AJs in epithelial cells.
Zebrafish CRY represses transcription mediated by CLOCK‐BMAL heterodimer without inhibiting its binding to DNA
Authors: Ishikawa Tomoko , Hirayama Jun , Kobayashi Yuri , Todo Takeshi
Published: March 2003

Background CLOCK and BMAL1 proteins, members of the basic helix‐loop‐helix PAS (PER‐ARNT‐SIM) superfamily of transcription factors which bind to the E‐box DNA motif, are required for the high‐level expression of the circadian clock genes period (per) and cryptochrome (cry). CRY inhibits transcriptional activity of the CLOCK‐BMAL1 heterodimer, generating a negative‐feedback loop that is the core element of the circadian oscillator.

Results: We show that zebrafish CRY (zCRY1a) neither disrupts the association between zfCLOCK and zfBMAL nor inhibits binding of the zfCLOCK‐zfBMAL heterodimer to an E‐box‐bearing DNA fragment. Instead it binds to the heterodimer to form a stable zCRY1a‐zfCLOCK‐zfBMAL‐E‐box complex. Another zebrafish CRY protein, zCRY4, does not have transcriptional inhibitor activity, whereas zCRY1a has strong activity. zCRY4 does not associate with zfCLOCK and zfBMAL. We also show that the presence of a chemical reductant in the reaction mixture is crucial for efficient binding of the CLOCK‐BMAL heterodimer to E‐box bearing DNA, which is indicative of the reduction/oxidation (redox)‐sensitive character of the heterodimer.

Conclusions: Our findings suggest that CRY represses CLOCK‐BMAL‐mediated transcription by interacting directly with the zfCLOCK‐zfBMAL–E‐box complex.
Two conserved structural components, A‐rich bulge and P4 XJ6/7 base‐triples, in activating the group I ribozymes
Authors: Ikawa Yoshiya , Yoshimura Takeshi , Hara Hidemi , Shiraishi Hideaki , Inoue Tan
Published: March 2003

Background: The A‐rich bulge of the group I intron ribozyme, a highly conserved structural element in its P5 peripheral region, plays a significant role in activating the ribozyme. The bulge has been known to interact with the P4 stem forming P4 XJ6/7 base‐triples in the conserved core. The base‐triples by themselves have also been identified as a distinctive element responsible for enhancing the activity of the ribozyme.

Results: A weakly active variant of the Tetrahymena ribozyme lacking the P5 extension was dramatically activated by the addition of an A‐rich bulge at the peripheral region, or by replacement of the original P4 XJ6/7 base‐triples in the core structure with more stabilized isosteric ones. Biochemical analyses showed that the two methods of activation affect the ribozyme differently.

Conclusions: The long‐range interaction between the A‐rich bulge and P4 or additionally stabilized P4 XJ6/7 base‐triples can contribute dramatically to activation of the Tetrahymena ribozyme. Both improve the kcat value, which represents the rate of the limiting step of the ribozyme reaction when its binding site is saturated with GTP. However, the bulge or the modified base‐triples gave a moderate reduction or considerable increase, respectively, to the Km(GTP) value.
Diversity of the cadherin‐related neuronal receptor/protocadherin family and possible DNA rearrangement in the brain
Authors: Yagi Takeshi
Published: March 2003

Both the brain and the immune systems are complex. The complexity is generated by enormously diversified single cells. In the immune system, extensive cell death, gene regulation of immunoglobulin (Ig) and T‐cell receptor (TCR) gene expression, and somatic rearrangement and mutations are known to generate an enormous diversity of lymphocytes. In this process, double‐strand DNA breaks (DSBs) and DSB repair play significant roles. These processes at a DNA level are also physiologically significant in the nervous system during neurogenesis, and chromosomal variations have been detected in the nucleus of differentiated neurones. In another parallel with the immune system, cadherin‐related neuronal receptors (CNRs) are diversified synaptic proteins. The CNR genes belong to protocadherin (Pcdh) gene clusters. Genomic organizations of CNR/Pcdh genes are similar to that of the Ig and TCR genes. Somatic mutations in and combinatorial gene regulation of CNR/Pcdh transcripts during neurogenesis have been reported. This review focuses on the diversity of the CNR/Pcdh genes and possible DNA diversification in the nervous system.
Instability of sensory histidine kinase mRNAs in Escherichia coli
Authors: Aiso Toshiko , Ohki Reiko
Published: March 2003

Background: Regulating mRNA stability is one of the essential mechanisms in gene expression. In order to identify genes from Escherichia coli whole genome whose expression is effectively modulated during the process of mRNA decay, we previously performed differential display‐PCR as the first step. In the screening, it was suggested that two mRNAs from the histidine kinase genes, narX and yojN, in a two‐component signal transduction system, were extremely unstable. In this study we analysed the stability of sensory kinase mRNAs, e.g. arcB, barA, rcsC, narQ, narX and evgS mRNA.

Results: The cellular level of the histidine kinase mRNAs was very low and the mRNAs were rapidly degraded in wild‐type cells cultured at 37 °C in LB medium. Additional experiments using RNase E deficient cells indicated that the mRNAs existed abundantly and expressed a prolonged half‐life in the cells. Monocistronic transcripts of the cognate response regulator genes, arcA, rcsB, narP and narL have a half‐life of 1.5–3.4 min.

Conclusions: mRNAs of the six histidine kinase genes in E. coli are synthesized efficiently, but rapidly degraded in wild‐type cells.
Comparative analysis of the self‐incompatibility (S‐) locus region of Prunus mume: identification of a pollen‐expressed F‐box gene with allelic diversity
Authors: Entani Tetsuyuki , Iwano Megumi , Shiba Hiroshi , Che Fang‐Sik , Isogai Akira , Takayama Seiji
Published: March 2003

Background: Self‐incompatibility (SI) in the Solanaceae, Rosaceae and Scrophulariaceae is gametophytically controlled by a single polymorphic locus, termed the S‐locus. To date, the only known S‐locus product is a polymorphic ribonuclease, termed S‐RNase, which is secreted by stylar tissue and thought to act as a cytotoxin that degrades the RNA of incompatible pollen tubes. However, understanding how S‐RNase causes S‐haplotype specific inhibition of pollen tubes has been hampered by the lack of a cloned pollen S‐determinant gene.

Results: To identify the pollen S‐determinant gene, we investigated the genomic structure of the S‐locus region of the S1‐ and S7‐haplotypes of Prunus mume (Japanese apricot), and identified 13 genes around the S‐RNase gene. Among them, only one F‐box gene, termed SLF (S‐locus F‐box), fulfilled the conditions for a pollen S‐determinant gene: (i) together with the S‐RNase gene, it is located within the highly divergent genomic region of the S‐locus, (ii) it exhibits S‐haplotype specific diversity among three analysed S‐haplotypes, and (iii) it is specifically expressed in pollen, but not in the styles or leaves.

Conclusion: The results indicate that SLF is a prime candidate for the pollen S‐determinant gene of SI.
Excursion guide 12: Yellowstone
Authors: WALTHAM TONY
Published: March 2003

The National Park at Yellowstone contains more than half the world's active geysers. Lying mostly in Wyoming, its host of geothermal features and fresh volcanic rocks offers an incomparable experience for any visiting geologist.
White Watson's Tablets
Authors: FORD TREVOR D.
Published: March 2003

The story of an innovation in the late 18th‐ to early 19th‐century development of geology.
Is pure groundwater safe to drink?: natural "contamination' of groundwater in Norway
Authors: Banks David , Midtg?rd Aase Kjersti , Morland Geir , Reimann Clemens , Strand Terje , Bjorvatn Kjell , Siewers Ulrich
Published: March 2003

The title of this article is designed to provoke. Naturally occurring parameters are, by definition, not contamination. Nevertheless, nature is not necessarily nice, and naturally occurring trace toxins can be every bit as undesirable as their counterparts derived from human pollution.
Interpreting geology at Portreath, Cornwall: a resource for geological education
Authors: Marks A.
Published: March 2003

The geology of Portreath preserved both in the natural outcrop and as building stones is assessed as a potential resource for visiting educational groups. Portreath is a former mining port, its expansion and historical development being closely associated with local and regional geology. A fieldwork programme and complementary literature search revealed that this location contains a wide range of accessible rock types suitable for student analysis.
A Farey story: the pioneer geologist John Farey (1766–1826)
Authors: Ford Trevor D. , Torrens Hugh S.
Published: March 2003

John Farey was a pioneer British geologist whose work has been too long overlooked. His only major geological publication was concealed in what appears to be a local report on the agriculture and minerals of Derbyshire, commissioned by the Board of Agriculture and published in three volumes between 1811 and 1817. Farey also published an extraordinary amount in periodicals and prepared a remarkable series of geological maps and cross‐sections which were never published, although a number of hand‐drawn copies circulated and undoubtedly influenced the rise of stratigraphical geology.
A Bayesian criterion for simplicity in inverse problem parametrization
Authors: Malinverno Alberto
Published: March 2003

To solve a geophysical inverse problem in practice means using noisy measurements to estimate a finite number of parameters. These parameters in turn describe a continuous spatial distribution of physical properties. (For example, the continuous solution may be expressed as the linear combination of a number of orthogonal functions; the parameters are the coefficients multiplying each of these functions.) As the solution is non-unique, estimating the parameters of interest also requires a measure of their uncertainty for the given data. In a Bayesian approach, this uncertainty is quantified by the posterior probability density function (pdf) of the parameters. This ‘parameter estimation’, however, can only be carried out for a given way of parametrizing the problem; choosing a parametrization is the ‘model selection’ problem.

The purpose of this paper is to illustrate a Bayesian model selection criterion that ranks different parametrizations from their posterior probability for the given set of geophysical measurements. This posterior probability is computed using Bayes’ rule and is higher for parametrizations that better fit the data, which are simple in that they have fewer free parameters, and which result in a posterior pdf that departs the least from what is expected a priori. Bayesian model selection is illustrated for a gravitational edge effect inverse problem, where the variation of density contrast with depth is to be inferred from gravity gradient measurements at the surface. Two parametrizations of the density contrast are examined, where the parameters are the coefficients of an orthogonal function expansion or the values at the nodes of a cubic spline interpolation. Bayesian model selection allows one to decide how many free parameters should be used in either parametrization and which of the two parametrizations is preferred given the data. While the illustration used here is for a simple linear problem, the proposed Bayesian criterion can be extended to the general non-linear case.
Nanoscale haematite–ilmenite lamellae in massive ilmenite rock: an example of ‘lamellar magnetism’ with implications for planetary magnetic anomalies
Authors: McEnroe S. A. , Harrison R. J. , Robinson Peter , Langenhorst Falko
Published: March 2003

Massive, nearly ‘pure’, haemo-ilmenite layers from historic ore deposits in Rogaland, Norway contain very few silicates or other oxides and typically produce remanence-dominated magnetic anomalies. These rocks are ideal for evaluating the magnetic properties of fine exsolution intergrowths and the larger titanohaematite lamellae in the host ilmenite grains. A typical bulk composition, Ilm 84, exsolved at high temperature to produce host ilmenite Ilm 94 and micron-sized haematite lamellae Ilm 23 as measured by electron microprobe (EMP). Subsequent undercooling of the ilmenite and the micron-scale haematite lamellae led to metastable nucleation of nanoscale lamellae down to unit-cell scale, leaving depleted hosts between lamellae with compositions of Ilm 98 and Ilm 15–13 as measured by TEM–EDX. Samples have high coercivities, and average NRM values of 25 A m−1, which typically show ∼2 per cent saturation in the NRM state. The amount of magnetization in these samples is too high to be solely accounted for by a spin-canted AF moment in the haematite. Based on Monte Carlo simulations of haematite–ilmenite interfaces at the atomic scale and on measured rock-magnetic properties, we predict that the magnetization is carried by a ferrimagnetic substructure produced at the contacts of the very fine-scale titanohaematite and ilmenite exsolution lamellae.
Constraining of the zero total surface charge in galvanic modelling
Authors: Hongisto H. , Oksama M.
Published: March 2003

The galvanic problem is frequently solved by a Fredholm integral equation of the second kind based on a single layer source formulation. At higher conductivity contrasts between the model and its surroundings the homogeneous part of the integral equation approaches an eigenvalue equation. With infinite contrast the solution of this limiting integral equation is non‐unique, but in the subspace of zero total charge the solution is unique. This mathematical property of the integral equation is reflected in its numerical solution with the result that large numerical errors may appear and convergence of the solution becomes very slow. Errors are, for the most part, related to the computed excess charge generated in the numerical solution. The effect is studied by comparing the results computed from the solution of the integral equation alone with those computed from a particular solution where the requirement of zero total charge is used as a constraint. The model examples clearly show that the use of the constraint condition significantly improves the accuracy of the results.
Some unintended features of elastic finite‐difference models
Authors: Wild A.J. , Singh S.C.
Published: March 2003

While finite‐difference methods have been used extensively for many years to model wave propagation in elastic media, some of the more subtle effects observable in such models are very inadequately documented in the geophysical literature, especially in regard to their practical numerical consequences.

In addition to the intended travelling waves, and the undesirable exponential instability revealed by the von Neumann test, typical second‐order‐time finite‐difference equations also support drifting linear solutions, as can be verified, both theoretically and by numerical experiment. The necessity of these solutions, and their relationship to the incompleteness of the set of travelling‐wave eigenfunctions of the finite‐difference operator, can be exposed by a matrix‐based analysis, and exact expressions for them can be obtained by using standard algebraic techniques.

A further peculiarity of the finite‐difference formulation is numerical anisotropy, which emerges in a grid of more than one spatial dimension, even when the modelled medium is intended to be isotropic. This anisotropy can be explained and quantified in terms of the exact eigenfunction solutions to the finite‐difference equation, which, it is found, can be obtained in a simple, closed form, for a typical modern 3D staggered scheme.
Magnetotelluric survey for exploration of a volcanic‐rock reservoir in the Yurihara oil and gas field, Japan*
Authors: Mitsuhata Yuji , Matsuo Koichi , Minegishi Masato
Published: March 2003

The Yurihara oil and gas field is located on the southern edge of Akita Prefecture, northeastern Japan. In this area, drilling, surface geological surveys and many seismic surveys have been used to investigate the geological structure. Wells drilled into the Nishikurosawa Basalt Group (NBG) of Miocene age found oil and gas reservoirs at depths of 1.5–2 km. Oil and gas are now being produced commercially and further exploration is required in the surrounding areas. However, since the neighbouring areas are covered with young volcanic products from the Chokai volcano, and have a rough topography, the subsurface distribution of the NBG must be investigated using other methods in addition to seismic reflection. According to the well data, the resistivity of the NBG is comparatively higher than that of the overlying sedimentary formations, and therefore the magnetotelluric (MT) method is expected to be useful for the estimation of the distribution of the NBG.

An MT survey was conducted along three survey lines in this area. Each line trended east–west, perpendicular to the regional geological strike, and was composed of about 25 measurement sites. Induction vectors evaluated from the magnetic field show that this area has a two‐dimensional structure. The evaluated resistivity sections are in agreement with the log data. In conclusion, we were able to detect resistive layers (the NBG) below conductive layers. The results indicate that the NBG becomes gradually less resistive from north to south. In the centre of the northern line, an uplifted resistive area is interpreted as corresponding to the reservoir. By comparison with a seismic section, we prove the effectiveness of the integration of seismic and MT surveys for the investigation of the morphology and internal structure of the NBG. On other survey lines, the resistive uplifted zones are interpreted as possible prospective areas.
Attenuation of P‐ and S‐waves in limestones
Authors: Assefa Solomon , McCann Clive , Sothcott Jeremy
Published: March 2003

Ultrasonic compressional‐ and shear‐wave attenuation measurements have been made on 40, centimetre‐sized samples of water‐ and oil‐saturated oolitic limestones at 50 MPa effective hydrostatic pressure (confining pressure minus pore‐fluid pressure) at frequencies of about 0.85 MHz and 0.7 MHz respectively, using the pulse‐echo method. The mineralogy, porosity, permeability and the distribution of the pore types of each sample were determined using a combination of optical and scanning electron microscopy, a helium porosimeter and a nitrogen permeameter. The limestones contain a complex porosity system consisting of interparticle macropores (dimensions up to 300 microns) and micropores (dimensions 5–10 microns) within the ooids, the calcite cement and the mud matrix. Ultrasonic attenuation reaches a maximum value in those limestones in which the dual porosity system is most fully developed, indicating that the squirt‐flow mechanism, which has previously been shown to occur in shaley sandstones, also operates in the limestones. It is argued that the larger‐scale dual porosity systems present in limestones in situ could similarly cause seismic attenuation at the frequencies of field seismic surveys through the operation of the squirt‐flow mechanism.
Sharp boundary inversion of 2D magnetotelluric data
Authors: Smith Torquil , Hoversten Michael , Gasperikova Erika , Morrison Frank
Published: March 2003

We consider 2D earth models consisting of laterally variable layers. Boundaries between layers are described by their depths at a set of nodes and interpolated laterally between nodes. Conductivity within each layer is described by values at a set of nodes fixed within each layer, and is interpolated laterally within each layer. Within the set of possible models of this sort, we iteratively invert magnetotelluric data for models minimizing the lateral roughness of the layer boundaries, and the lateral roughness of conductivities within layers, for a given level of data misfit. This stabilizes the inverse problem and avoids superfluous detail. This approach allows the determination of boundary positions between geological units with sharp discontinuities in properties across boundaries, while sharing the stability features of recent smooth conductivity distribution inversions.

We compare sharp boundary inversion results with smooth conductivity distribution inversion results on a numerical example, and on inversion of field data from the Columbia River flood basalts of Washington State. In the synthetic example, where true positions and resistivities are known, sharp boundary inversion results determine both layer boundary locations and layer resistivities accurately. In inversion of Columbia flood basalt data, sharp boundary inversion recovers a model with substantially less internal variation within units, and less ambiguity in both the depth to base of the basalts and depth to resistive basement.
On the aperture effect in 3D Kirchhoff‐type migration
Authors: Sun Jianguo
Published: March 2003

It is well known that the migrated image given by a Kirchhoff‐type (diffraction‐stack) migration with limited aperture is always accompanied by some events which depend on the migration aperture. Although these events may severely affect the quality of migration, they have been studied only in 2D cases. Here, the events due to the migration aperture in 3D situations are investigated using a new method of analysing the reconstructed wavefield. It is found that a finite migration aperture results in a reconstructed wavefield with two components. One comes from the tangent points and curves between the traveltime surfaces of reflected and point‐diffracted rays and is independent of the migration aperture, and the other is from the boundary of the migration aperture and depends strongly on the location and size as well as on the shape of the migration aperture. It is this last component that describes the aperture effect in migration. If the migration aperture is not sufficiently large, and if the input for migration is not zero on the boundary of the migration aperture, the boundary component may partially or totally cancel the migration signal. Furthermore, for synthetic data, the aperture effect cannot be eliminated by enlarging the migration aperture because, except for the common‐shotpoint data, the aperture effect always exists however large the migration aperture becomes. This leads to the conclusion that the published Kirchhoff‐type operators are not the exact inverse operators of the Fresnel–Kirchhoff integral if the input data are synthetic.
On the interference of man‐made EM fields in the magnetotelluric ‘dead band’
Authors: Iliceto  , Santarato
Published: March 2003

During processing of magnetotelluric (MT) data, acquired in a survey carried out in southern Italy, a problem was encountered, connected with the so‐called ‘dead band’ of the MT signal (around 1 Hz). In the apparent resistivity curves of some MT soundings, a V‐shaped minimum appeared, centred on the dead‐band frequency. This phenomenon turned out to originate from a strong artificial source and was not due to a downward bias of the robust processing techniques adopted. The source distance from the MT sounding locations was such that the V‐shaped minimum fell precisely in the dead‐band frequency range. Theoretical considerations about fields generated by an electric dipole led us to the probable identification of the source as the d.c.‐powered railway between Naples and Bari.
Geophone orientation and coupling in three‐component sea‐floor data: a case study
Authors: Li Xiang‐Yang , Yuan Jianxin
Published: March 2003

We analyse the geophone orientation and coupling in a data set from the North Sea. Based on the polarization of the water‐break on the sea‐floor, we have derived processing algorithms for determining the receiver orientation for gimballed and non‐gimballed geophone systems. For a gimballed system, the problem reduces to a simple horizontal rotation. However, for a non‐gimballed system, where all three geophone axes may vary due to varying acquisition conditions such as dipping sea‐floor, twisting of recording cable, etc., the three orientation angles cannot be found directly from the recorded displacement vectors. Using the data redundancy within a common‐receiver gather, a robust two‐stage method is derived for the non‐gimballed system in which all three orientations can initially be unknown. Testing on the North Sea data set acquired with a gimballed system shows that the three‐component geophones in the data set are orientated satisfactorily within an error of 5°. However, there are some undesirable cross‐couplings between the vertical and horizontal geophones, which results in leakage of shear‐wave energy from the horizontal components to the vertical components.