bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of caudal autotomy on locomotor performance in a viviparous skink, Niveoscincus metallicus
Authors: Chapple D. G. , Swain R. 
Published: March 2003

Summary

Tail loss has repeatedly been associated with the impairment of locomotor performance in lizards. However, although the immediate impact of tail loss may be severe, most previous studies have failed to establish how long such locomotory costs persist.
We investigated both the short‐term (24–36 h) and long‐term (4 and 12 weeks) consequences of tail loss on locomotor performance in a viviparous ground‐dwelling skink, Niveoscincus metallicus (O’Shaughnessy 1874). Sprint speed, climbing ability and stamina were measured as performance variables. The locomotor performance of both adult males and pregnant females were tested during the study.
Male and female lizards responded differently to tail loss, although the immediate impact of autotomy on performance was generally minor. In males caudal autotomy imposed a significant immediate impact on sprint speed, while in females stamina was reduced immediately after autotomy.
Females regenerated their tails significantly faster than males. Recovery of locomotor performance over the 3‐month duration of the study was observed in females (for endurance capacity) but not males (for sprint speed).
Overall, the impact of tail loss on locomotor performance was generally limited or short‐lived in N. metallicus.
Regulation of intrinsic terminator by translation in Escherichia coli: transcription termination at a distance downstream
Authors: Abe Hiroyuki , Abo Tatsuhiko , Aiba Hiroji 
Published: March 2003

Background:Rho‐independent terminators in Escherichia coli are DNA sequences of 30–50 bp consisting of a GC‐rich dyad symmetry sequence followed by a run of T residues in the nontemplate strand. The transcription termination at the Rho‐independent terminator occurs within the T‐tract in vitro. It has been believed that the transcription termination at the Rho‐independent terminator occurs within the T‐tract in vivo, as established in vitro, and therefore the 3′ ends of mRNAs are mostly generated as a direct result of transcription termination. However, how the transcription termination occurs and how the 3′ ends of mRNAs are formed in living cells remains to be studied.Results:We developed a double terminator system in which a second Rho‐independent terminator was placed downstream of the crp terminator. This system made it possible to detect transcripts that pass through the crp terminator by Northern blotting. We found that most of the crp transcripts extend beyond the crp terminator. The transcriptional read‐through at the crp terminator was reduced when the translation of crp mRNA was interrupted. The level of the read‐through transcript decreased with distance between the two terminators, suggesting that transcription termination occurs at multiple positions beyond the crp terminator.Conclusion:We conclude that most RNA polymerase reads through the crp terminator in the natural situation and terminates transcription over a wide region downstream of the crp terminator, resulting in heterogeneous primary transcripts that are subsequently processed back to the terminator hairpin. We propose that ribosome translation to the crp stop codon causes read‐through of the terminator. The regulatory effect of translation on Rho‐independent termination may be a general phenomenon at other operons.
Transposition of IS1 circles
Authors: Shiga Yasuyuki , Sekine Yasuhiko , Ohtsubo Eiichi 
Published: March 2003

BackgroundIS1, the smallest active transposable element in bacteria, encodes transposase. IS1 transposase promotes transposition as well as production of miniplasmids from a plasmid carrying IS1 by deletion of the region adjacent to IS1. The IS1 transposase also promotes production of IS1 circles consisting of the entire IS1 sequence and a sequence, 6–9 bp in length, as a spacer between terminal inverted repeats of IS1. The biological significance of the generation of IS1 circles is not known.ResultsPlasmids carrying an IS1 circle with a spacer sequence 6–9 bp long transposed to target plasmids at a very high frequency when transposase was produced from a co‐resident plasmid. The products were target plasmids with the donor plasmid inserted at the ends of IS1 in the IS1 circle. This insertion accompanied the removal of the spacer sequence and duplication of the sequence at the target site. IS1 circles with a much longer spacer sequence transposed less frequently. The SOS response was induced in cells harbouring a plasmid with an IS1 circle owing to transposase. IS1 circles could transpose in the strain deficient in H‐NS, a nucleoid‐associated DNA‐binding protein known to be required for the transposition of IS1.ConclusionsIS1 circles appear to act as intermediates for simple insertion into the target DNA via cleavage of the circles which induces the SOS response. H‐NS may function in promoting the assembly of an active IS1 DNA‐transposase complex at the terminal inverted repeats.
Presence of telomeric G‐strand tails in the telomerase catalytic subunit TERT knockout mice
Authors: Yuan Xunmei , Ishibashi Shun , Hatakeyama Shinji , Saito Motoki , Nakayama Jun‐ichi , Nikaido Rika , Haruyama Takahiro , Watanabe Yoshifumi , Iwata Hijiri , Iida Mari , Sugimura Haruhiko , Yamada Nobuhiro , Ishikawa Fuyuki 
Published: March 2003

BackgroundTelomerase consists of two essential subunits, the template RNA (TR; telomerase RNA) and the catalytic subunit TERT (telomerase reverse transcriptase). Knockout mice with a mTR (mouse TR) deletion have been described and well characterized. However, mice with a mTERT (mouse TERT) deletion have not been reported.Results mTERT‐knockout mice have been constructed. The first generation mTERT −/− mice were fertile, and did not show any noticeable macroscopic or microscopic phenotypic change. All tissue cells derived from mTERT −/− mice that were examined lacked telomerase activity, indicating that mTERT is the only gene encoding the telomerase catalytic subunit. Pulse field gel electrophoresis (PFGE) and nondenaturing in‐gel hybridization analyses showed that mouse telomeric DNA has G‐strand 5′‐overhangs, as demonstrated for human and yeast cells. This telomeric single‐stranded G‐tail was also observed in MEF (mouse embryonic fibroblast) and liver cells derived from mTERT −/− mice.Conclusions mTERT‐knockout mice show phenotypes that are apparently normal at least during the early generations. This observation is similar to that obtained with the mTR‐knockout mice. The presence of the telomeric G‐strand tails in mTERT −/− mice suggests that these telomeric 5′‐overhangs are produced by telomerase‐independent mechanisms, as has been proposed for yeast and human.
LUCA15, a putative tumour suppressor gene encoding an RNA‐binding nuclear protein, is down‐regulated in ras‐transformed Rat‐1 cells
Authors: Edamatsu Hironori , Kaziro Yoshito , Itoh Hiroshi 
Published: March 2003

BackgroundThe proliferation of mammalian cells is controlled by various intracellular mitogenic signalling pathways. In the intracellular pathways, Ras is involved in the activation of proto‐oncogenes such as an immediate early gene c‐fos. The somatic mutations of ras genes that elicit the constitutive activation of Ras have been found in tumours. Although these findings suggest that the constitutive activation of Ras‐mediated pathways alters the expression of a set of genes involving tumorigenesis, these genes have not yet fully been studied.ResultsTo study the up‐ or down‐regulated genes in ras‐transformed cells, we analysed Rat‐1 transfectants expressing Ras(G12V) mutant protein in response to isopropyl‐1‐β‐thio‐
D‐galactoside using a differential display. We found that the mRNA level of rat homologue of LUCA15, which has been cloned initially as a putative tumour suppressor gene mapped on human chromosome 3, was down‐regulated by the expression of Ras(G12V). Epitope‐tagged LUCA15 protein was localized in nuclei and had the ability to bind poly(G) RNA homopolymers in vitro. Moreover, ectopic expression of LUCA15 in human fibrosarcoma HT1080 cells suppressed the cell growth.ConclusionThese results demonstrate that LUCA15 is one of the down‐regulated genes in ras‐transformed cells, and suggests that LUCA15 may function as a negative regulator of cell proliferation by the alteration of its mRNA level.
Genetic dissection of SecA: suppressor mutations against the secY205 translocase defect
Authors: Matsumoto Gen , Nakatogawa Hitoshi , Mori Hiroyuki , Ito Koreaki 
Published: March 2003

The driving force for protein translocation across the bacterial plasma membrane is provided by SecA ATPase, which undergoes striking conformational changes characterized by the membrane insertion and deinsertion cycle. This action of SecA requires the membrane‐embedded SecYEG complex. Previously, we have identified a cold‐sensitive secY mutation (secY205), affecting the most carboxy‐terminal cytosolic domain, that did not allow an ATP‐dependent insertion of a SecA‐preprotein complex. Thus, this mutant provides an excellent system for genetic analysis of the SecY–SecA interaction.We carried out a systematic isolation of secA mutations that suppressed secY205 cold‐sensitivity. A total of 40 independent suppressor mutations were classified into: (i) allele‐specific suppressors, acting only against secY205, and (ii) ‘super active’ suppressors, acting against almost any sec defects. The former class of mutations, presumably with specific effects on the SecY–SecA interaction, clustered in two regions close to the Walker motif A sequences of the two ATP‐binding domains. The latter mutations, enhancing general SecA activities, were mostly in or around the minor ATP‐binding domain.The Walker motif A regions of SecA are important for the SecA–SecY interaction that leads to the SecA conformational changes required for insertion into the SecYEG channel. The minor ATP‐binding domain is important for the down‐regulation of SecA activities.
Fission yeast homologues of the B′ subunit of protein phosphatase 2A: multiple roles in mitotic cell division and functional interaction with calcineurin
Authors: Tanabe Osamu , Hirata Dai , Usui Hirofumi , Nishito Yasumasa , Miyakawa Tokichi , Igarashi Kazuhiko , Takeda Masao 
Published: March 2003

BackgroundProtein phosphatase 2A (PP2A) is a serine/threonine phosphatase distributed in eukaryotes from yeast to human, and plays pivotal roles in diverse cellular functions such as metabolism, cell cycle progression, gene expression and development. PP2A holoenzyme is a heterodimer of a catalytic subunit C and a regulatory subunit A, or a heterotrimer of C, A and a variable regulatory subunit consisting of three families; B, B′, and PR72. Specific functions for each variable subunit are not well understood.Results Two fission yeast genes pbp1+ and pbp2+ homologous to the regulatory subunit B′ were isolated. Physical in vivo interaction of the gene products with the catalytic subunit was demonstrated. A double disruption haploid mutant (Δpbp1Δpbp2) showed growth defect, cell shape and size abnormality, multiseptation and anucleated cell formation due to abnormality in septum positioning. These phenotypes were suppressed by human B′ cDNA, indicating the striking conservation of the B′ function from yeast to human. Over‐expression of fission yeast B′ led to growth defects, a loss of cell shape polarity, septal abnormality and anucleated cell formation. Δpbp1Δpbp2 and pbp1 null haploids were hypersensitive to calcineurin inhibitors, cyclosporin A and FK506, with which the mutants underwent arrest at post‐anaphase and cell lysis. Double disruption of calcineurin and pbp1+, but not pbp2+, genes led to synthetic lethality.Roles of B′ and its functional interaction with calcineurin in fission yeast. This hypothetical summary scheme is depicted based on the observations in this study and others (Jiang & Hallberg 2000; Sugiura et al. 1998; Yoshida et al. 1994). CAB′ is the trimeric holoenzyme of PP2A containing B′ as a variable regulatory subunit.imageConclusionThe fission yeast B′ subunit of PP2A plays critical roles in cell shape control and septum formation, and shares essential functions with calcineurin for viability, possibly through their roles in cytokinesis and cell wall integrity.
Over‐expression of DREF in the Drosophila wing imaginal disc induces apoptosis and a notching wing phenotype
Authors: Yoshida Hideki , Inoue Yoshihiro H. , Hirose Fumiko , Sakaguchi Kengo , Matsukage Akio , Yamaguchi Masamitsu 
Published: March 2003

Background DNA replication‐related element binding factor (DREF) has been suggested to be involved in regulation of DNA replication‐ and proliferation‐related genes in Drosophila. While the effects on the mutation in the DNA replication‐related element (DRE) in cultured cells have been studied extensively, the consequences of elevating wild‐type DREF activity in developing tissues have hitherto remained unclear.Results We over‐expressed DREF in the wing imaginal disc using a GAL4‐UAS targeted expression system in Drosophila. Over‐expression of DREF induced a notching wing phenotype, which was associated with ectopic apoptosis. A half reduction of the reaper, head involution defective and grim gene dose suppressed this DREF‐induced notching wing phenotype. Furthermore, this was also the case with co‐expression of baculovirus P35, a caspase inhibitor. In addition, over‐expression of the 32 kDa boundary element‐associated factor (BEAF‐32), thought to compete against DREF for common binding sites in genomic regions, rescued the DREF‐induced notching wing phenotype, while a half reduction of the genomic region, including the BEAF‐32 gene, exerted enhancing effects. To our knowledge, this is the first evidence for a genetic interaction between DREF and BEAF‐32.Conclusion The DREF‐induced notching wing phenotype is caused by induction of apoptosis in the Drosophila wing imaginal disc.
Generalized Dix equation and analytic treatment of normal‐moveout velocity for anisotropic media*
Authors: Grechka Vladimir , Tsvankin Ilya , Cohen Jack K. 
Published: March 2003

Despite the complexity of wave propagation in anisotropic media, reflection moveout on conventional common‐midpoint (CMP) spreads is usually well described by the normal‐moveout (NMO) velocity defined in the zero‐offset limit. In their recent work, Grechka and Tsvankin showed that the azimuthal variation of NMO velocity around a fixed CMP location generally has an elliptical form (i.e. plotting the NMO velocity in each azimuthal direction produces an ellipse) and is determined by the spatial derivatives of the slowness vector evaluated at the CMP location. This formalism is used here to develop exact solutions for the NMO velocity in anisotropic media of arbitrary symmetry.For the model of a single homogeneous layer above a dipping reflector, we obtain an explicit NMO expression valid for all pure modes and any orientation of the CMP line with respect to the reflector strike. The contribution of anisotropy to NMO velocity is contained in the slowness components of the zero‐offset ray (along with the derivatives of the vertical slowness with respect to the horizontal slownesses) — quantities that can be found in a straightforward way from the Christoffel equation. If the medium above a dipping reflector is horizontally stratified, the effective NMO velocity is determined through a Dix‐type average of the matrices responsible for the ‘interval’ NMO ellipses in the individual layers. This generalized Dix equation provides an analytic basis for moveout inversion in vertically inhomogeneous, arbitrarily anisotropic media. For models with a throughgoing vertical symmetry plane (i.e. if the dip plane of the reflector coincides with a symmetry plane of the overburden), the semi‐axes of the NMO ellipse are found by the more conventional rms averaging of the interval NMO velocities in the dip and strike directions.Modelling of normal moveout in general heterogeneous anisotropic media requires dynamic ray tracing of only one (zero‐offset) ray. Remarkably, the expressions for geometrical spreading along the zero‐offset ray contain all the components necessary to build the NMO ellipse. This method is orders of magnitude faster than multi‐azimuth, multi‐offset ray tracing and, therefore, can be used efficiently in traveltime inversion and in devising fast dip‐moveout (DMO) processing algorithms for anisotropic media. This technique becomes especially efficient if the model consists of homogeneous layers or blocks separated by smooth interfaces.The high accuracy of our NMO expressions is illustrated by comparison with ray‐traced reflection traveltimes in piecewise‐homogeneous, azimuthally anisotropic models. We also apply the generalized Dix equation to field data collected over a fractured reservoir and show that P‐wave moveout can be used to find the depth‐dependent fracture orientation and to evaluate the magnitude of azimuthal anisotropy.
AVO investigations of shallow marine sediments
Authors: Riedel M. , Theilen F. 
Published: March 2003

Amplitude‐variation‐with‐offset (AVO) analysis is based on the Zoeppritz equations, which enable the computation of reflection and transmission coefficients as a function of offset or angle of incidence. High‐frequency (up to 700 Hz) AVO studies, presented here, have been used to determine the physical properties of sediments in a shallow marine environment (20 m water depth). The properties that can be constrained are P‐ and S‐wave velocities, bulk density and acoustic attenuation. The use of higher frequencies requires special analysis including careful geometry and source and receiver directivity corrections. In the past, marine sediments have been modelled as elastic materials. However, viscoelastic models which include absorption are more realistic. At angles of incidence greater than 40°, AVO functions derived from viscoelastic models differ from those with purely elastic properties in the absence of a critical angle of incidence. The influence of S‐wave velocity on the reflection coefficient is small (especially for low S‐wave velocities encountered at the sea‐floor). Thus, it is difficult to extract the S‐wave parameter from AVO trends. On the other hand, P‐wave velocity and density show a considerably stronger effect. Attenuation (described by the quality factor Q) influences the reflection coefficient but could not be determined uniquely from the AVO functions. In order to measure the reflection coefficient in a seismogram, the amplitudes of the direct wave and the sea‐floor reflection in a common‐midpoint (CMP) gather are determined and corrected for spherical divergence as well as source and streamer directivity. At CMP locations showing the different AVO characteristics of a mud and a boulder clay, the sediment physical properties are determined by using a sequential‐quadratic‐programming (SQP) inversion technique. The inverted sediment physical properties for the mud are: P‐wave velocity α=1450±25 m/s, S‐wave velocity β=90±35 m/s, density ρ=1220±45 kg/m3, quality factor for P‐wave QP=15±200, quality factor for S‐wave QS=10±30. The inverted sediment physical properties for the boulder clay are: α=1620±45 m/s,β=360±200 m/s,ρ=1380±85 kg/m3,QP=790±660,QS=25±10.
Avoiding pitfalls of least‐squares inversion by using the energy‐flux error criterion
Authors: Causse Emmanuel 
Published: March 2003

ABSTRACTSeismic inversion by modelling and data fitting depends on the criterion chosen to measure the misfit between observed and modelled data. The popular least‐squares error criterion has an important drawback: it is sensitive both to the shape of the recording surface and to velocity variations along this surface. Tests on synthetic seismic reflection data show that least‐squares inversion may work surprisingly poorly in situations where (i) the range of angles between reflected rays and the acquisition surface is large, (ii) the velocity varies significantly along this surface, or (iii) a compensation for the effects of dissipation is applied to the gradients. In these situations, the gradients may contain important artefacts and have incorrect amplitudes. The outgoing flux of energy of the residual wavefield across the acquisition surface provides an alternative measure of the data misfit which is independent of the recording surface, provided this surface is closed, and which is only sensitive to the aperture in the practical situation of an open surface or line of receivers. Energy‐flux inversion presents a strong resemblance to reverse‐time migration, but with the additional possibility of iteratively improving the images. In all the tests, energy‐flux inversion provided better images than least‐squares inversion.
Seismic endoscopy: multi‐offset multi‐azimuth imaging around boreholes – data processing and experimental results
Authors: Nicollin Florence , Conil Frédéric , Gibert Dominique 
Published: March 2003

An acoustic method, called seismic endoscopy, able to perform 3D imaging around shallow‐depth boreholes is presented. A probe, composed of an isotropic source and a directional receiver working in the 20–100 kHz frequency range, provides images of cylindrical volumes having radii of a few metres, with an accuracy of centimetres and 25° azimuthal directivity. In order to obtain clear images of the medium discontinuities, multi‐offset and multi‐azimuth data acquisition allows specific algorithms to be used to determine vertical directivity correction, azimuthal focusing and reflected wave enhancement by cancellation of the tube waves. The method is tested with data acquired in an acoustic tank and with synthetic data. Initial experimental results at a test site demonstrate the performance of the seismic endoscopy probe.