bluuebunny/crossref_metadata_2025 huggingface dataset:
A yeast gene product, Fob1 protein, required for both replication fork blocking and recombinational hotspot activities
Authors: Kobayashi Takehiko , Horiuchi Takashi
Published: November 2003

Background:  In the rRNA gene cluster on the Saccharomyces cerevisiae chromosome XII, a unique site that blocks progression of the replication fork exists in a single unit of the repeats. The site RFB (replication fork blocking) is located within one of two cis‐elements present in a nontranscribed region of each repeated unit, which are required for obtaining maximal activity of a hotspot (HOT1) dependent recombination.

Results:  To investigate the correlation between replication fork blocking at RFB and homologous recombination at HOT1, we have isolated Hot1‐defective mutants and examined their ability for fork blocking at RFB. Amongst 23 isolated mutants, four were found to be defective in both abilities. Genetic analysis of the mutants reveals that a single mutation, named fob1 (fork blocking less), is responsible for the defects in both abilities. The FOB1 gene is located on chromosome IV and has no homology with any other genes listed in DNA data banks.

Conclusion:  The pleiotropic effect of the fob1 mutation suggests that homologous recombination at HOT1 is closely linked with DNA replication fork blocking event at RFB.
Subunit assembly in vivo of Escherichia coli RNA polymerase: role of the amino‐terminal assembly domain of alpha subunit
Authors: Kimura Makoto , Ishihama Akira
Published: November 2003

Background: The RNA polymerase core enzyme of Escherichia coli is assembled in the sequence α→α2→α2β→α2 ββ′. The amino‐terminal domain down to residue 235 of the Escherichia coli RNA polymerase α subunit plays a key role in enzyme assembly. In vitro reconstitution studies from mutant α subunits have indicated the involvement of multiple sites for α dimerization, two regions (one near residue 45 and the other near residue 80) for β association, and two regions (one around residue 80 and the other between residues 180 and 200) for β′ association. The mechanism of RNA polymerase assembly in vivo, however, remains largely unknown.

Results: RNA polymerase assembly in vivo was analysed for E. coli strains carrying expression plasmids for four amino‐terminal deletion and 11 Ala‐Ser (AS) dipeptide‐insertion mutant α subunits. For detection of RNA polymerase complexes, a hexa‐histidine (H6) tag was added to all these mutant α at their carboxy‐termini, and subunit complexes containing the H6‐tagged α were isolated by passing cell extracts through Ni2+‐affinity columns. The assembly properties of most α mutants were consistent with those observed in in vitro reconstitution studies. Some mutants defective in β′ association in vitro such as those carrying mutations at residues 80 and 200 were, however, assembled in vivo, suggesting that a specific condition(s) or factor(s) supports RNA polymerase assembly in vivo. One possible candidate supporting the RNA polymerase assembly is the molecular chaperon(s), because DnaK (hsp70) was always associated with assembly‐defective RNA polymerase mutants. Most assembly competent mutants complemented two temperature‐sensitive mutant alleles of rpoA, but two assembly competent mutants, one (αΔN20) carrying a deletion at the extreme amino‐terminal region and the other (αI‐60) with AS insertion at residue 60, failed to complement these ts mutants. The failure suggests that these assembly competent but complementation‐negative α mutants lack an as yet unidentified function(s). In the case of these two mutants, DnaK was associated, with apparently assembled RNA polymerase.

Conclusion: The α–α, α–β and α–β′ contact sites on the RNA polymerase α subunit identified in in vitro reconstitution studies also participate in the subunit assembly in vivo. Some α mutants defective in assembly in vitro are, however, assembled in vivo. A factor(s) such as the molecular chaperon DnaK or a specific intracellular condition(s) may affect RNA polymerase assembly in vivo.
Initiation of Sendai virus multiplication from transfected cDNA or RNA with negative or positive sense
Authors: Kato Atsushi , Sakai Yuko , Shioda Tatsuo , Kondo Toru , Nakanishi Mahito , Nagai Yoshiyuki
Published: November 2003

Background: The mononegavirus superfamily (Mononegavirales) comprises three families, Rhabdoviridae, Paramyxoviridae and Filoviridae. These viruses possess a single stranded negative sense RNA as the genome. Recent success in the recovery of infectious virus from a transfected cDNA of mononegaviruses including Sendai virus, a prototypic paramyxovirus, is opening the possibility of their genetic engineering. However, infectious viruses have been recovered only by initiating the infectious cycle with cDNA directing the synthesis of antigenomic positive sense (+) RNA. Starting with genomic negative sense (−) RNA has been unsuccessful. Furthermore, the recovery efficiency has often been extremely low.

Results: We describe here an analogous system that allows recovery of Sendai virus at a high rate, from cells in which the transfected cDNA and plasmids to support the synthesis of viral nucleocapsid protein and RNA polymerases are coexpressed by vaccinia virus‐driven bacteriophage T7 polymerase. Our system was able to recover the virus from cDNA directing not only (+)RNA but also (−)RNA. Moreover, using this system, we succeeded in recovery of the virus by transfection of in vitro synthesized (+)RNA or (−)RNA. This improved virus recovery appeared to be accomplished by supplying the supporting plasmids at an optimal ratio and by minimizing the cytopathic effect of the vaccinia virus by specific inhibitors. In addition, it was probably critical that our cDNAs were constructed to generate viral authentic RNAs without adding T7 promoter‐specific nucleotides to the 5′ ends. An immediate application of the system was demonstrated by the creation of a candidate vaccine strain with a predetermined attenuating mutation in the cleavage‐activation site of the viral fusion glycoprotein.

Conclusion: We have established methods which greatly improve the recovery of Sendai virus from cDNA. There is essentially no absolute obstacle to recovery of the virus from the (−)RNA template. Even the complete full length RNA chain in the naked form appears to be properly encapsidated to become a functional template.
Introns and gene evolution
Authors: De Souza Sandro J. , Long Manyuan , Gilbert Walter
Published: November 2003

In one scenario of gene evolution, exon shuffling has a fundamental role in increasing gene diversity. As DNA sequences accumulate in the databases, the picture of the intron/exon structures of genes becomes more and more clear. We discuss in this review some features of this picture that suggest that introns have been present since the early stages of evolution, and that exon shuffling was a fundamental process in the construction of ancient as well as modern genes.
Signalling from endoplasmic reticulum to nucleus: transcription factor with a basic‐leucine zipper motif is required for the unfolded protein‐response pathway
Authors: Mori Kazutoshi , Kawahara Tetsushi , Yoshida Hiderou , Yanagi Hideki , Yura Takashi
Published: November 2003

Background: Accumulation of unfolded proteins in the endoplasmic reticulum (ER) triggers the transcriptional induction of molecular chaperones and folding enzymes localized in the ER. Thus, eukaryotic cells possess an intracellular signalling pathway from the ER to the nucleus, called the unfolded protein‐response (UPR) pathway. In Saccharomyces cerevisiae, such induction is mediated by the cis‐acting unfolded protein‐response element (UPRE) which has been thought to be recognized by one or more transcription factor(s).

Results: Extensive mutational analysis revealed that UPRE contains a partial palindrome with a spacer of one nucleotide (CAGCGTG) that is essential for its function. We then cloned the ERN4 (presumably identical with HAC1) gene using yeast one‐hybrid screening, in which the GAL4‐ERN4 fusion gene constitutively activates the UPR pathway. The ERN4 gene encodes a basic‐leucine zipper protein (Ern4p) that specifically binds to UPRE in vitro and activates transcription in vivo. Cells lacking Ern4p are unable to induce transcription of any of the five target genes tested and exhibit sensitivity to ER stress and inositol requirement for growth.

Conclusion: We concluded that Ern4p represents a major component of the putative transcription factor (UPRF) responsible for the UPR leading to the induction of ER‐localized stress proteins.
Essential role of active nuclear transport in apoptosis
Authors: Yasuhara Noriko , Eguchi Yutaka , Tachibana Taro , Imamoto Naoko , Yoneda Yoshihiro , Tsujimoto Yoshihide
Published: November 2003

Background
: Apoptosis is defined by chromatin condensation, nuclear fragmentation and the formation of apoptotic bodies. Because apoptotic signals are transmitted through a common pathway that includes the target steps of death‐driving ICE‐family proteases and anti‐cell death protein Bcl‐2 in the cytoplasm, the signals must be transferred from the cytoplasm to the nucleus, at least to induce the apoptotic manifestation of the nucleus. Small signal molecules might diffuse across nuclear pores, but larger molecules are transported by active mechanisms requiring ATP and GTP hydrolysis. It is not known whether apoptotic signals are transmitted into the nucleus by the mechanisms of active nuclear transport.

Results
: To test the possibility that active nuclear transport is involved in apoptotic signal transmission, we have analysed the effects of molecules that inhibit active nuclear transport on apoptosis. Wheat germ agglutinin (WGA), excess amounts of p10 protein, Ran‐GTPγS complex, and anti‐PTAC58 antibody, which all inhibit active nuclear transport when exogenously microinjected, prevent Fas‐induced apoptotic nuclear manifestation. WGA also prevents apoptotic nuclear change promoted by microinjected active CPP32β/Yama protease (an ICE family member), which plays an essential role in most apoptosis.

Conclusions
: The results presented here strongly suggest that active nuclear transport is essential for apoptotic signal transduction.
Transcriptional activation through interaction of MBF2 with TFIIA
Authors: Li Feng‐Qian , Takemaru Ken‐ichi , Goto Masahide , Ueda Hitoshi , Handa Hiroshi , Hirose Susumu
Published: November 2003

Background: Transcriptional activation of the Drosopohila melanogaster fushi tarzu gene by FTZ‐F1 or its silkworm counterpart BmFTZ‐F1 requires two cofactors MBF1 and MBF2 which do not directly bind to DNA. MBF1 is a bridging molecule that connects FTZ‐F1 (or BmFTZ‐ F1), MBF2 and TATA binding protein TBP. MBF2 is a positive cofactor that activates transcription.

Results: To elucidate the mechanism of transcriptional activation by MBF2, we isolated a cDNA coding for the factor. Northern blot analyses showed temporally restricted expression of MBF2 mRNA similar to that of BmFTZ‐F1 mRNA. The cDNA sequence predicts a polypeptide of 10 kDa whereas natural MBF2 is a glycoprotein of 22 kDa. The deduced amino acid sequence of the factor showed no homology with proteins in the databases. Farwestern analyses and glutathione S–transferase interaction assays demonstrated that MBF2 makes a direct contact with the β‐subunit of TFIIA. In a HeLa cell nuclear extract, bacterially expressed recombinant MBF2 activated transcription from various promoters as natural MBF2 did. This activation requires the MBF2–TFIIA interaction. When recombinant MBF2 was added to the HeLa cell nuclear extract in the presence of MBF1 and FTZ622 bearing the DNA‐binding region of FTZ‐F1, it selectively activated transcription of the fushi tarazu gene. This selective activation also requires the MBF2–TFIIA interaction.

Conclusion: MBF2 activates transcription through its interaction with TFIIA. Selective transcriptional activation occurs when MBF2 is recruited to a promoter carrying the FTZ‐F1 binding site by FTZ‐F1 and MBF1.
Microtubule‐associated coiled‐coil protein Ssm4 is involved in the meiotic development in fission yeast
Authors: Yamashita Akira , Watanabe Yoshinori , Yamamoto Masayuki
Published: November 2003

Background: In fission yeast, an RNA species named meiRNA is specifically required for the promotion of the first meiotic division. To dissect the function of this RNA and its partner RNA‐binding protein Mei2, we screened for high‐copy‐number suppressors of the arrest prior to the first meiotic division caused by loss of meiRNA.

Results: Analysis of one of the suppressors, named ssm4, suggested that it encodes a coiled‐coil protein carrying a microtubule‐binding motif at its N‐terminus. Expression of ssm4 was restricted to cells undergoing meiosis. Disruption of ssm4 affected neither vegetative growth nor conjugation, but resulted in frequent generation of asci carrying less than four spores. Tagged Ssm4 could colocalize with microtubules in mitotic cells, and was seen to localize at spindles during both the first and the second meiotic division. The microtubule‐binding motif was essential for the association of Ssm4 with microtubules and for its function during meiosis, but not for the suppression of loss of meiRNA. Ssm4 appeared to possess a potential to migrate to the nucleus.

Conclusions: Ssm4 is a microtubule‐colocalizing protein that plays a role specifically in meiosis. Ssm4 appears to modify the structure or the function of nuclear microtubules in order to promote the meiotic nuclear division.
Identification of an extended half‐site motif required for the function of peroxisome proliferator‐activated receptor α
Authors: Osada Shiho , Tsukamoto Toshiro , Takiguchi Masaki , Mori Masataka , Osumi Takashi
Published: November 2003

Background:

Peroxisome proliferator‐activated receptors (PPARs) belong to the nuclear hormone receptor superfamily and regulate many genes of the proteins involved in lipid metabolism, including peroxisomal acyl‐CoA oxidase (AOX). Through heterodimerization with retinoid X receptors (RXRs), PPAR was believed to recognize the sequence elements consisting of two directly repeating 6‐bp half‐sites spaced by one nucleotide (DR‐1), located in the regulatory regions of these genes.

Results:

Employing the peroxisome proliferator‐responsive enhancer of the rat AOX gene, we analysed the minimal sequence requirements for enhancer activity and PPARα/RXRα binding. We found that the sequence just downstream of the DR‐1 motif is indispensable for both functions. By a direct selection procedure of high‐affinity binding sites from a random sequence pool, we identified a consensus sequence at the four positions next to DR‐1. We also suggest that PPARα binds to the downstream half‐site, whereas RXRα binds to the upstream half‐site of the AOX DR‐1.

Conclusions:

An extended half‐site of 10‐bp, but not a simple 6‐bp half‐site, is required for the PPARα binding, upon heterodimer formation with RXRα. The binding polarity of PPARα/RXRα seems to be opposite to that of other RXR‐involving heterodimers.
The duplex DNA is very underwound in the three‐stranded RecA protein‐mediated synaptic complex
Authors: Voloshin Oleg N. , Camerini‐Otero R. Daniel
Published: November 2003

Background:

The RecA protein is a central player in bacterial homologous recombination. It promotes two key events: the search for homology between two DNA molecules and the subsequent formation of the synaptic complex composed of RecA and three DNA strands (two from one duplex and one single strand). In spite of numerous studies, the architecture of the synaptic complex is still far from clear.

Results:

We have exploited two approaches to study the structure of Escherichia coli RecA protein‐mediated DNA synapsis: chemical modification with potassium permanganate and treatment of synaptic complexes of different lengths with topoisomerase I. The linking number difference values, obtained after separation of the individual sets of topoisomers in an agarose gel, were used to determine the number of bases per helical turn. We were able to show that the topology of the three‐stranded complexes containing RecA is quite different from that expected for deproteinized D‐loops. The original duplex in the synaptic complex is unwound, but not necessarily unpaired, to a structure topologically equivalent to DNA with approximately 27 bp per turn. Despite the fact that the patterns of reactivity towards potassium permanganate cannot be interpreted unambiguously, the results of chemical footprinting can be explained in terms of a synaptic complex as an extended and unwound three‐stranded helical structure.

Conclusions:

This work provides the first quantitative topological parameters for the RecA protein‐mediated three‐stranded synaptic complex. Furthermore, the structure of synaptic complexes is different from that of a simple D‐loop.
A complete Not I restriction map covering the entire long arm of human chromosome 11
Authors: Hosoda Fumie , Arai Yasuhito , Kitamura Eiko , Inazawa Johji , Fukushima Michiyo , Tokino Takashi , Nakamura Yusuke , Jones Carol , Kakazu Naoki , Abe Tatsuo , Ohki Misao
Published: November 2003

Background:

Human chromosome 11 is one of the autosomes on which many disease genes have been mapped. Many different types of map, including a radiation hybrid map, a genetic map, and an STS‐content YAC map, have been constructed for the chromosome. However, a physical map providing accurate physical distances has not yet been established. A chromosome‐wide Not I restriction map was constructed to understand the overall feature of the genome organization and to facilitate the positional cloning of disease genes.

Results:

A complete Not I restriction map of the entire long arm of human chromosome 11 was constructed using linking‐clone mapping. This physical map covers 77.6 Mb, from a pericentromeric Not I site to the terminus, and provides the most accurate ordering and distance estimation to date. We also mapped 138 sequence markers in the q13 region that have been poorly mapped previously.

Conclusions:

The restriction map of the entire long arm of human chromosome 11 is the longest restriction map of the human genome. This mapping has disclosed unique features regarding the organization of the chromosome, indicating that restriction sites of Not I, a CpG‐recognition enzyme, are primarily distributed in R (or T) bands and that genetic distance is considerably longer in R (or T) bands than in G bands. The mapping, as well as the dense concentration of mapped markers within the q13 region, should help with positional cloning of the genes associated with various diseases.
Activators and repressors: making use of chromatin to regulate transcription
Authors: Wolffe Alan P. , Wong Jiemin , Pruss Dmitry
Published: November 2003

Metazoans and yeast use enzymes that modulate histone acetylation and nucleosomal integrity in order to regulate transcription. Repressor complexes deacetylate histones and stabilize nucleosomes. Activator complexes acetylate histones and disrupt nucleosomes. Variation in chromatin structure makes a major contribution to gene regulation. Here we discuss the enzymatic complexes and molecular machines that make use of chromatin to control transcription.
Two mechanisms in the action of repressor δEF1: binding site competition with an activator and active repression
Authors: Sekido Ryohei , Murai Kasumi , Kamachi Yusuke , Kondoh Hisato
Published: November 2003

Background:

Counteraction between activators and repressors is crucial for the regulation of a number of cell‐specific enhancers, where an activator and a repressor are mutually competitive in binding to the same site. δEF1 is a repressor protein of δ1‐crystallin minimal enhancer DC5 binding at the CACCT site, and inhibits activator δEF3 from binding to the overlapped site. It has two zinc finger clusters N‐fin and C‐fin, close to N‐ and C‐termini, respectively, and a homeodomain in the middle. δEF1 also binds to the E2‐box sequence CACCTG, and represses E2‐box‐dependent enhancers.

Results:

The mechanism of the repressor action of δEF1 was investigated by examining various deletion mutants of δEF1 for their activity to repress δ1‐crystallin enhancer fragment HN which contained DC5 sequence and an additional activator site. Both zinc finger clusters were found to be essential for DNA binding and repression, but the homeodomain was not. In addition, the NR domain close to the N‐terminus was required for full repression. The NR domain showed active repression when fused to the Gal4 DNA binding domain. Active repression by δEF1, dependent on the NR domain, was also demonstrated in a situation where the binding sites of δEF1 and δEF3 were separated.  N‐fin and C‐fin in their isolated forms bind the 5′‐(T/C)ACCTG‐3′ and 5′‐(t/C)ACCT‐3′ sequences, respectively, while the homeodomain showed no DNA binding activity. An analysis of DNA binding of the ΔIntF form, having both N‐fin and C‐fin, indicated that a single DNA binding domain is assembled from two zinc finger clusters.

Conclusion:

Two mechanisms are involved in the repressor action of δEF1. First, a binding site competition with an activator which depends on the integrity of both zinc finger clusters, and second, an active repression to silence an enhancer which is attributed to the NR domain.
Roles of TraI protein with activities of cleaving and rejoining the single‐stranded DNA in both initiation and termination of conjugal DNA transfer
Authors: Fukuda Hirokazu , Ohtsubo Eiichi
Published: November 2003

Background:

The plasmid R100 encodes the TraI protein, which is required for conjugal DNA transfer. TraI has the activity of site‐ and strand‐specific nicking of the supercoiled plasmid DNA. The molecular mechanism of this specific nicking, which is supposed to be the initiation reaction of DNA transfer, is not understood.

Results:

We have demonstrated that TraI has the ability to cleave the single‐stranded DNA at the same site as the nicking site (nic) in a region, which we here refer to as sbi. The product contained the TraI protein which was covalently linked to the newly generated 5′ end of the nicking reaction. Both the cleaving and nicking reactions took place under almost the same conditions and required the presence of the sbi region. DNase I‐footprinting analysis revealed that the TraI bound to the single‐stranded DNA of the sbi region. TraI did not cleave the double‐stranded DNA fragment, but it did cleave the double‐stranded DNA with a single‐stranded DNA portion in the sbi region. KMnO4 mapping analysis revealed that TraI can melt the sbi region in the supercoiled DNA to generate a single‐stranded portion. We have also demonstrated that TraI was able to rejoin the cleaved products. The rejoining reaction required the 5′ end of one cleaved product with the TraI covalently attached and the 3′ end of the other product containing the sbi region.

Conclusions:

Our results demonstrate that the nicking reaction—the initiation reaction of DNA transfer—is actually the cleaving reaction of the single‐stranded DNA. TraI, which has both cleaving and rejoining activities, is thought to be involved in the termination of DNA transfer, to give a copy of the conjugative plasmid by joining the 5′ end, which is generated by the initiation reaction, with the 3′ end, which will be generated upon cleavage of the sbi region appearing after one round of the rolling circle replication of the plasmid.
Regions of the Escherichia coli primary sigma factor σ70 that are involved in interaction with RNA polymerase core enzyme
Authors: Nagai Hiroki , Shimamoto Nobuo
Published: November 2003

Background:

The σ factors of bacterial RNA polymerase are required for recognition of promoters in transcription initiation. Most σ factors share several regions with significant homology in their amino acid sequences (regions 1–4). Some primary σ factors carry a large nonconserved segment between regions 1 and 2. The binding of an σ factor to the core enzyme alters the structure and properties of the σ factor, but little is known about the binding mechanism and subsequent reactions. In this report, we employed the protein footprinting method to investigate the alteration of the structure and function of Escherichia coli σ70 by binding to core enzyme and promoter DNA.

Results:

A segment between regions 1.1 and 1.2, and that in region 3.2, were preferentially cleaved by hydroxyl radicals. Upon binding to the core enzyme, segments in regions 1.1, 2, 3 and 4 were substantially protected, while cleavage at a small segment in region 4.2 was weakly enhanced. In a binary complex of holoenzyme and promoter DNA, additional segments in regions 2.4 and 4.2 were protected, while the protection at region 1.1 disappeared. The nonconserved acidic region of σ70 in the holoenzyme became hypersensitive upon binding to DNA.

Conclusions:

These results suggest that not only the conserved region 2, but also regions 1.1, 3 and 4 of the σ factor are involved in binding to the core enzyme. The nonconserved acidic region is likely to be more exposed by further binding of σ factor to promoter DNA.
Role of the Drosophila EGF receptor in determination of the dorsoventral domains of escargot expression during primary neurogenesis
Authors: Yagi Yoshimasa , Hayashi Shigeo
Published: November 2003

Background
: Primary neurogenesis in the central nervous system of insects and vertebrates occurs in three dorsoventral domains in each side of the neuroectoderm. Among the three dorsoventral domains of the Drosophila neuroectoderm, the medial and lateral columns express the zinc‐finger gene escargot (esg), whereas the intermediate column does not. We studied esg expression as a probe to investigate the mechanism of neuroectoderm patterning.

Results
: The effect of dorsoventral patterning genes on esg expression was studied. decapentaplegic, snail and twist were found to repress esg expression outside the neuroectoderm. The expression of esg in the intermediate column is normally repressed, but was de‐repressed when the EGF receptor homologue (DER) activity was either elevated or reduced. A neurogenic enhancer of esg was identified, and was shown to be separable into a distal region that promotes ubiquitous expression in the neuroectoderm and a proximal region that represses the intermediate expression.

Conclusions
: decapentaplegic, snail, twist and an activator act through the distal region to initiate transcription of esg in the neuroectoderm. We propose that the combination of opposing gradients of DER and its ligand creates a peak of DER activity in the intermediate column where DER represses esg transcription through the proximal repressor region. These two kinds of regulation establish the early esg expression that prefigures the neuroectoderm patterning.
Involvement of the MRE2 gene of yeast in formation of meiosis‐specific double‐strand breaks and crossover recombination through RNA splicing
Authors: Nakagawa Takuro , Ogawa Hideyuki
Published: November 2003

Background
: The mre2 mutant of Saccharomyces cerevisiae is defective in meiotic recombination and produces inviable spores, but the sensitivities to DNA damaging agents, methyl methanesulphonate and ultraviolet light are not altered by the mutation. Mre2 has two copies of RNA recognition motif (RRM), suggesting its participation in RNA metabolism in meiosis.

Results
: An amino acid substitution in the N‐terminal RRM of Mre2 confers a meiotic recombination defect. Using this mre2N strain, the MER2 gene was isolated as a multi‐copy suppressor of the recombination defect. Meiosis‐specific splicing of MER2 pre‐mRNA was impaired in the mre2 deletion (mre2Δ) mutant. The mre2Δ mutant was defective in the formation of meiosis‐specific double‐strand breaks (DSBs) and crossover and noncrossover recombinants. When the chromosomal MER2 gene was replaced with the intronless derivative of MER2 gene, cMER2, the formation of DSBs and of noncrossover recombinants were restored in the mre2Δ mutant. However, the amount of crossover recombinants produced in the mre2ΦcMER2 strain was ≈30% that in the wild‐type. In addition, the mre2ΔcMER2 mutant was defective in chromosome segregation and in viable spore formation.

Conclusions
: Mre2 participates in the formation of DSBs through meiosis‐specific splicing of MER2 pre‐mRNA. Besides, Mre2 is also involved in crossover recombination, possibly through splicing of RNA from another gene(s).
Phenotypic analysis of null mutants for DE‐cadherin and Armadillo in Drosophila ovaries reveals distinct aspects of their functions in cell adhesion and cytoskeletal organization
Authors: Oda Hiroki , Uemura Tadashi , Takeichi Masatoshi
Published: November 2003

Background
: DE‐cadherin is an epithelial cadherin in Drosophila, and forms adherens junctions by associating with Armadillo (β‐catenin). To investigate its role in oogenesis, we generated germ‐line clones homozygous for a null mutation in shotgun (shg) encoding this molecule, and examined their phenotypes, comparing with those of armadillo (arm) mutants.

Results
: In the wild‐type ovaries, DE‐cadherin was expressed by both the germ‐line and somatic derivatives, colocalizing with Armadillo. In the shg mutant ovaries in which the mutation was restricted to the germ line, germ cells were rounded, and generated gaps between themselves, suggesting that their surface adhesiveness was reduced or lost. However, the positioning of germ cells in the egg chamber was normal. Two groups of somatic follicle cells—the border cells and centripetal follicle cells—frequently migrated along incorrect pathways, indicating that DE‐cadherin is required for their appropriate migration. Notably, the shg phenotypes were distinct from those of arm null mutants. Intercellular adhesion appeared to be less severely affected by arm than by the shg mutation, and the actin‐based cytoskeleton and cell arrangement were disorganized only in the arm mutants.

Conclusions
: These findings suggest that DE‐cadherin is critical for cell–cell adhesion, and functional to a certain extent without Armadillo, whereas Armadillo is required for cytoskeletal organization and for the control of cell positioning. We therefore propose that the molecular complex of DE‐cadherin and Armadillo which is present in normal cells is endowed with multiple functions derived from each molecule.
Molecular properties of the proteasome activator PA28 family proteins and γ‐interferon regulation
Authors: Tanahashi Nobuyuki , Yokota Kin‐ya , Ahn Joon Young , Chung Chin Ha , Fujiwara Tsutomu , Takahashi Ei‐ichi , DeMartino George N. , Slaughter Clive A. , Toyonaga Tetsushi , Yamamura Ken‐ichi , Shimbara Naoki , Tanaka Keiji
Published: November 2003

Background: Recent cDNA cloning of two homologous proteasome activators, PA28α and PA28β, indicated the presence of a structurally related third protein, Ki antigen, but a functional relationship between Ki antigen and the two PA28 proteins is unknown. Accumulating evidence has implicated an important role for PA28 in the major histocompatibility complex (MHC) class I‐restricted antigen processing pathway. Recently, an immunomodulatory cytokine γ‐interferon (γ‐IFN) was found to increase greatly the messages for PA28α and PA28β, but not Ki antigen, in human cells.

Results: Ki antigen was co‐immunoprecipitated with the 20S proteasome by anti‐proteasome antibody, and associated reversibly with the 20S proteasome, as observed for PA28α and PA28β. Therefore, Ki antigen was renamed PA28γ. Anti‐PA28γ antibody, however, did not immunoprecipitate PA28α and PA28β. γ‐IFN caused an almost complete loss of the PA28γ protein in cells without affecting its mRNA level, whereas the levels of both mRNA and protein for PA28α and PA28β were coordinately up‐regulated by γ‐IFN. Finally we showed that the human chromosomal genes of PA28α and PA28γ were located on 14q11.2 and 17q21.32‐21.33, respectively.

Conclusion: PA28γ (equivalent to Ki antigen) is a new member of the PA28 family proteins. It exists as a unique homopolymer under non‐denaturing conditions. γ‐IFN was found to induce the expression of PA28α and PA28β, whereas it caused almost complete loss of the PA28γ protein in cells. The reciprocal expression of the PA28 family proteins may imply their involvement in distinct biological processes.
Basal level transcription of the human hsp86 gene is directed by intron‐based elements
Authors: Lange Peer , Victor Martin , Benecke Bernd‐Joachim
Published: November 2003

Background: The heat shock response includes the syntheses of three major size‐classes of heat shock proteins (hsps) designated as class 20, 70 and 90 hsps, respectively. In contrast to the class 20 and 70 hsp genes, those coding for the class 90 hsps are already actively transcribed in the non‐induced state.

Results: We have shown that the increased basal level transcription of the human hsp86 gene depends on the presence of the first intron. Furthermore, intron I of the hsp86 gene was also capable of conferring increased basal level transcription on the human hsp70 promoter. Finally, the intron I‐based sequence elements of the hsp86 gene mediated an effective rescue of 5′‐truncated hsp70 and hsp86 promoters. In contrast, such a rescue of inactivated promoters was not obtained with the viral SV40 gene enhancer which is often also capable of stimulating basal level expression.

Conclusions: Element(s) which direct the basal transcription of the human hsp86 gene at normal physiological temperatures are located within the first intron of the gene. It is conceivable that this intron‐dependent activation of basal hsp86 transcription reflects a fundamental requirement for this protein in the context of cellular growth and metabolism under non‐stress conditions.
Signal transduction via the histidyl‐aspartyl phosphorelay
Authors: Egger Linda A. , Park Heiyoung , Inouye Masayori
Published: November 2003

The histidyl‐aspartyl phosphorelay, formerly described as the two‐component system, is the predominant mode of signal transduction in bacteria. Adaptation to environmental changes occurs through a sensor histidine protein kinase and a response regulator. The histidine protein kinase is usually a transmembrane receptor and the response regulator is a cytoplasmic protein. Together the histidyl‐aspartyl phosphorelay proteins mediate reversible phosphorylation events that control downstream effectors. Following autophosphorylation at a conserved histidine residue, the histidine kinase serves as a phospho‐donor for the response regulator. Once phosphorylated, the response regulator mediates changes in gene expression or cellular locomotion. The EnvZ‐OmpR phosphorelay system in Escherichia coli, which monitors external osmolarity and responds by differentially modulating the expression of the OmpF and OmpC major outer membrane porins, will be described as a model system. While histidine kinases were thought to be present only in prokaryotes, they have recently been identified in eukaryotic systems. Here, we review the unique and conserved features of this growing family of signal transducers.
atonal is a proneural gene for a subset of olfactory sense organs in Drosophila
Authors: Gupta Bhagwati Prasad , Rodrigues Veronica
Published: November 2003

Background: The antenna of the adult fruit fly, Drosophila melanogaster, is covered with three morphologically distinct types of olfactory sense organs. In addition, mechano‐ and hygro‐sensitive receptors are also present on its surface. While much has been learnt about the development of peripheral nervous system in Drosophila, the mechanisms underlying the development of olfactory sensilla are just beginning to be unraveled. The antennal sense organs have several properties that make them distinct from other sense organs. While each sensillum type is arranged in a well‐defined region of the antenna, the position of an individual sensillum is not fixed. The development of these sense organs appears to combine an initial step of cell recruitment, as in photoreceptors, followed by cell lineage mechanisms, as in the development of other external sense organs. The earliest step in development, the selection of a sensory organ precursor, involves the interaction of proneural and neurogenic genes. The proneural gene for the antennal sense organs has been elusive so far.

Results: We show that the basic helix‐loop‐helix (bHLH) transcription factor encoded by atonal (ato) is a proneural gene for one morphological type of olfactory sensilla on the antenna and for all the olfactory sensilla on the maxillary palp. Loss of function and overexpression experiments together reveal that ato is both necessary and sufficient to specify these sensilla. Immunohistochemical experiments show that Ato expresses in a dynamic pattern in the developing antennal disc.

Conclusions: Our results demonstrate that ato acts solely in the specification of antennal sensilla coeloconica. This along with our previous observation that the AS‐C genes do not function in antenna allows us to suggest that other proneural genes must operate in the specification of sensilla basiconica and trichoidea. Our experiment involving overexpression of extramacrochaetae, a negative regulator of bHLH encoding genes, results in a significant reduction in the number of all three types of antennal sensilla. This suggests that the unidentified proneural gene(s) possibly encode bHLH factors.
Capelinhos: The disappearing volcano
Authors: COLE DUNCAN GUEST PAUL, ANGUS, JOHN
Published: November 2003

The 1957–58 eruption of Capelinhos, on Faial, in the Azores, built a new volcano at the west end of the island. Erosion by the sea has subsequently destroyed over two‐thirds of this structure and will probably continue to remove much of the rest of the volcano over the next few decades.
Very large landslides in the Himalayas
Authors: WALTHAM TONY
Published: November 2003

Landslides are a major component of geomorphological processes on the steep slopes of the Himalayan mountains. Three slides in the Annapurna region demonstrate a sequence from large to very large failures.
Lake District pioneers – the earliest footprints on land
Authors: Johnson Eric W. , Briggs Derek E.G. , Wright Joanna L.
Published: November 2003

New evidence reveals that the first arthropods colonized dry land over 450 million years ago, more than 20 million years before the appearance of vascular plants. Traditionally, it was thought that animals only emerged on to land after plants had become established, thus providing a plentiful new food source. The earliest known terrestrial trace fossils occur in volcanogenic sediments from the English Lake District. The trace fossils are thought to have been made on land by a small millipede‐like creature. These rocks contain no other fossils.
There's a ratfish in our cellar!
Authors: Ahlberg Per Erik , Coates Michael I.
Published: November 2003

A crushed fossil fish‐head, discovered on a Lower Carboniferous flagstone from the Isle of Man, proves to be the only known articulated specimen of the early ratfish Psammodus. This is a major discovery, which promises to cast light on a key episode in the evolution of shark‐like fishes.
Britain's oldest rocks
Authors: ROLLINSON HUGH
Published: November 2003

In August 1994, Britain's top science journal, Nature, announced that a team of scientists working at the University of Cambridge had found Europe's oldest rocks at a remote location near to Gruinard Bay in the Scottish Highlands. They reported ancient volcanic rocks with an age of 3300 million years. This was more than 300 million years older than any age previously measured on rocks in the British Isles and between 100 and 200 million years older than any rocks known in Europe. The discovery of itself is in many ways unremarkable, for much older rocks are known from ancient continental shield areas in Canada, Australia and Greenland. What was important was that the reported age did not agree with any of the other measured ages known within the British Isles. This was highlighted in a comment in the same issue of Nature, which suggested that the new data were so important that they require a massive revision of our views on the earliest history of the British Isles. For other scientists, however, the conflict between these new data and previously reported ages began to raise questions about the methods employed in dating the ‘oldest rocks’.
THE IMPORTANCE OF TOPOGRAPHIC CORRECTIONS ON MAGNETOTELLURIC RESPONSE DATA FROM RUGGED REGIONS OF ANATOLIA
Authors: Gürer Aysan , Metin Ìlkışık O.
Published: November 2003

Topographic irregularities cause some distortions of magnetotelluric (MT) fields. In the vicinity of a topographic feature, the TM‐mode distortion increases with the height and inclination of the slope. It is well‐known that TM‐mode (E⊥) topographic effects are much greater than TE‐mode (Eı) distortions.  We have made a study of MT anomalies in TM‐mode due to two‐dimensional topography. In order to reduce these effects, the distortion tensor stripping technique was used. After corrections, the resulting data can be interpreted as if they were obtained over a flat surface and depend only on the subsurface structure. However, this technique sometimes causes some geometrical distortions of the real subsurface structure.  One of our aims is to overcome this failure. We have modified the correction coefficients by considering the actual one‐dimensional geology. Model studies showed that our approach is especially useful in removing the terrain effects on complex 2D subsurface structures.  The other purpose of this study is to emphasize the importance of a proper terrain correction for data from sites having mountainous topography over complex geology, e.g. strike‐slip faults, suture zones and rift valleys. Some examples of MT data sets collected from the North Anatolian Fault Zone and from the thrust regions of the Western Taurides will be presented.
Fractured reservoir delineation using multicomponent seismic data
Authors: Li Xiang‐Yang
Published: November 2003

The characteristic seismic response to an aligned‐fracture system is shear‐wave splitting, where the polarizations, time‐delays and amplitudes of the split shear waves are related to the orientation and intensity of the fracture system. This offers the possibility of delineating fractured reservoirs and optimizing the development of the reservoirs using shear‐wave data. However, such applications require carefully controlled amplitude processing to recover properly and preserve the reflections from the target zone. Here, an approach to this problem is suggested and is illustrated with field data.  The proposed amplitude processing sequence contains a combination of conventional and specific shear‐wave processing procedures. Assuming a four‐component recording (two orthogonal horizontal sources recorded by two orthogonal horizontal receivers), the split shear waves can be simulated by an effective eigensystem, and a linear‐transform technique (LTT) can be used to separate the recorded vector wavefield into two principal scalar wavefields representing the fast and slow split shear waves. Conventional scalar processing methods, designed for processing P‐waves, including noise reduction and stacking procedures may be adapted to process the separated scalar wavefields. An overburden operator is then derived from and applied to the post‐stacked scalar wavefields. A four‐component seismic survey with three horizontal wells drilled nearby was selected to illustrate the processing sequence. The field data show that vector wavefield decomposition and overburden correction are essential for recovering the reflection amplitude information in the target zone. The variations in oil production in the three horizontal wells can be correlated with the variations in shear‐wave time‐delays and amplitudes, and with the variations in the azimuth angle between the horizontal well and the shear‐wave polarization. Dim spots in amplitude variations can be correlated with local fracture swarms encountered by the horizontal wells. This reveals the potential of shear waves for fractured reservoir delineation.
Direct interpretation of magnetotelluric sounding data based on the frequency‐normalized impedance function
Authors: Başokur Ahmet T. , Kaya Cemal , Ulugergerli Emin U.
Published: November 2003

An important aspect of any non‐linear inversion method is the generation of a suitable or good initial model as this controls the rate of convergence and accuracy of the result. To overcome the problem, a numerical method is presented for direct interpretation of magnetotelluric sounding data based on the frequency‐normalized impedance (FNI) function. The expressions used to calculate the parameters are developed, first for a two‐layer case under the assumption that deeper layers do not contribute to the early part of the FNI curve, and they are then generalized for an n‐layer situation. The parameters of the first layer are computed by using successive sample values and the final estimate is obtained from the arithmetic mean of selected values by excluding unacceptable results in the logarithmic space. The top layer is then removed using a reduction equation. The repetition of the procedure on successive branches of the FNI function gives successive layer parameters, the resistivity of the substratum being obtained at the final step, when the reduction equation becomes equal to the square root of that resistivity.  The proposed method can be used as a complementary method for iterative inversion as it creates an initial guess which is close to the optimal solution. The solution produced by the direct interpretation may also be modified by the interpreter to incorporate prior geological information before being input to iterative interpretation schemes.
Automated trend reinforcement of aeromagnetic data
Authors: Keating Pierre
Published: November 2003

Aeromagnetic maps poorly represent lineaments that are at acute angles to the flight‐line direction. Commonly used gridding algorithms cannot cope with local trends, magnetic anomalies at an angle with the main trend of the map, and tend to generate closed contours around the flight lines. By introducing some a priori information, it is possible to add extra data between the flight lines, i.e. trend lines, to reinforce local trends. The proposed automated technique is based on a nearest neighbour search of the maxima and minima in the aeromagnetic map. The resulting map is more realistic and derived maps, such as vertical gradients and analytical signal maps, are greatly improved. Moreover, this automated procedure is user independent and easy to implement. The technique is demonstrated on aeromagnetic data from the Kirkland Lake region, in north‐eastern Ontario, Canada.
Cross‐well seismic tomographic delineation of mineralization in a hard‐rock environment
Authors: Cao Shunhua , Greenhalgh Stewart
Published: November 2003

Seismic first‐arrival times from a cross‐well experiment are inverted by an iteratively reweighted least squares method for the velocity distribution between boreholes. The inversion is carried out in a multiresolution manner in which long wavelength features are reconstructed first and short wavelength features are gradually introduced into the solution model. As such, the inverse problem is overdetermined at the beginning and becomes mixed‐determined as the constraint on the solution is relaxed. The reconstruction procedure is independent of the initial model and very robust. An accurate and efficient first‐break traveltime calculation scheme is employed to eliminate the possibility of phase mismatches, which can arise with traditional ray shooting or bending methods. Shot static delays are included with the model parameters as unknowns and are recovered simultaneously with the velocity distribution.