bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional analysis of the C‐terminal cytoplasmic region of the M‐factor receptor in fission yeast
Authors: Hirota Kouji , Tanaka Kayoko , Watanabe Yoshinori , Yamamoto Masayuki 
Published: March 2003

BackgroundYeast mating‐pheromone receptors facilitate the study of G protein‐coupled signal transduction. To date, molecular dissection of the budding yeast α‐factor receptor has been done extensively, but little analysis has been performed with pheromone receptors of fission yeast, another genetically tractable yeast species.ResultsWe analysed the fission yeast M‐factor receptor Map3p. Truncation of the C‐terminal 54 amino acids made Map3p dominant‐negative over the wild‐type. This form, called Map3‐dn9p, was competent in the induction of pheromone‐dependent gene expression, although it could not direct proper conjugation. Map3‐dn9p failed both to provoke the orientated projection of conjugation tubes and to induce adaptation to the pheromone signal associated with endocytosis of the receptor. Deletion and substitution analyses suggested that the integrity of the C‐terminal region, rather than a specific subgroup of amino acid residues therein, was vital for the respective Map3p activities. Ubiquitination of the C‐terminus was not absolutely essential for Map3p function.ConclusionsThe C‐terminal region of Map3p is dispensable for the pheromone signalling per se, but is pivotal for adaptation and pheromone‐induced conjugation tube formation, as is true with the budding yeast α‐factor receptor. However, the mechanisms which induce adaptation appear to differ between fission and budding yeast concerning the necessity of ubiquitination.
Initial process of polyglutamine aggregate formation in vivo
Authors: Kimura Yoko , Koitabashi Sumiko , Kakizuka Akira , Fujita Takashi 
Published: March 2003

Background Polyglutamine expansion in protein is responsible for several inherited neuro‐degenerative diseases. The expansion has toxic effects on neural cells as well as results in forming aggregates. Using yeast, we examined the initial process of polyglutamine aggregate formation in vivo.Results Following expression, polyglutamine tracts were of a soluble form during a lag period, and then formed insoluble complexes. The lag was prolonged and the formation of insoluble complex became slower by decreasing the number of polyglutamine tracts and by a treatment with guanidine hydrochloride. Gel filtration analysis revealed that the soluble polyglutamine existed in a small form. Formation of polyglutamine aggregates appeared to follow similar kinetics reported in the in vitro studies, where polyglutamine tracts self‐aggregate in a length‐, concentration‐ and time‐dependent manner. However, in vivo, Hsp104 was required for the conversion from a soluble to an insoluble state. Without Hsp104, polyglutamine tracts tended to remain in a small soluble form, prolonging the lag. Moreover, the dependency on Hsp104 for aggregate formation was strong with the short polyglutamine tract, and decreased with the long polyglutamine tract.Conclusion For polyglutamine aggregate formation, a balance of parameters including the length of the polyglutamine tract, Hsp104, and level of polyglutamine expression determined its efficiency.
Cell culture analysis of the regulatory frameshift event required for the expression of mammalian antizymes
Authors: Howard Michael T. , Shirts Brian H. , Zhou Jiadong , Carlson C. Lance , Matsufuji Senya , Gesteland Raymond F. , Weeks Reitha S. , Atkins John F. 
Published: March 2003

Background Antizyme is a critical regulator of cellular polyamine levels due to its effect on polyamine transport and its ability to target ornithine decarboxylase for degradation. Antizyme expression is autoregulatory, through dependence on an unusual +1 translational frameshift mechanism that responds to polyamine levels.Results HEK293 cells were depleted of polyamines by treatment with an ornithine decarboxylase inhibitor, difluoromethylornithine (DFMO), and grown in the presence or absence of exogenous polyamines prior to the analysis of ribosomal frameshifting levels. Results obtained using an optimized dual luciferase assay system reveal a 10‐fold dynamic range of frameshifting, which correlates positively with polyamine addition. Polyamine addition to cells, which have not been pre‐treated with DFMO, also resulted in an increase in antizyme frameshifting but to a lesser degree (1.3 to 1.5‐fold). In addition, the constructs with the 3′ deletion were more responsive to stimulation by polyamine addition than those with the 5′ deletion.Conclusions The observed regulation of antizyme frameshifting demonstrates the efficiency of a polyamine homeostatic mechanism, and illustrates the utility of a quantifiable cell‐based assay for the analysis of polyamines or their analogues on translational frameshifting.
Circadian rhythm of aromatic l‐amino acid decarboxylase in the rat suprachiasmatic nucleus: gene expression and decarboxylating activity in clock oscillating cells
Authors: Ishida Yoshiki , Yokoyama Chihiro , Inatomi Tsutomu , Yagita Kazuhiro , Dong Xin , Yan Lily , Yamaguchi Shun , Nagatsu Ikuko , Komori Takahide , Kitahama Kunio , Okamura Hitoshi 
Published: March 2003

AbstractBackground: Aromatic l‐amino acid decarboxylase (AADC) is the enzyme responsible for the decarboxylation step in both the catecholamine and indoleamine synthetic pathways. In the brain, however, a group of AADC containing neurones is found outside the classical monoaminergic cell groups. Since such non‐monoaminergic AADC is expressed abundantly in the suprachiasmatic nucleus (SCN), the mammalian circadian centre, we characterized the role of AADC in circadian oscillation.
Results :
AADC gene expression was observed in neurones of the dorsomedial subdivision of the SCN and its dorsal continuant in the anterior hypothalamic area. These AADC neurones could uptake exogenously applied L‐DOPA and formed dopamine. AADC was co‐expressed with vasopressin and the clock gene Per1 in the neurones of the SCN. Circadian gene expression of AADC was observed with a peak at subjective day and a trough at subjective night. The circadian rhythm of AADC enzyme activity in the SCN reflects the expression of the gene.Conclusions: Non‐monoaminergic AADC in the SCN is expressed in clock oscillating cells, and the decarboxylating activity of master clock cells are under the control of the circadian rhythm.
SsrA‐mediated protein tagging in the presence of miscoding drugs and its physiological role in Escherichia coli
Authors: Abo Tatsuhiko , Ueda Koji , Sunohara Takafumi , Ogawa Kazuko , Aiba Hiroji 
Published: March 2003

AbstractBackground: We have shown recently that read‐through of a normal stop codon by a suppressor tRNA in specific genes possessing a Rho‐independent terminator leads to SsrA‐mediated tagging of extended proteins in Escherichia coli cells. Miscoding antibiotics such as kanamycin and streptomycin reduce translational fidelity by binding to the 30S ribosomal subunit. The aim of the present study was to address how miscoding antibiotics affect the read‐through of stop codons and SsrA‐mediated protein tagging.Results: Miscoding antibiotics caused translational read‐through of stop codons when added to the culture medium at sublethal concentrations. Under the same conditions, the drugs enhanced SsrA‐mediated tagging of bulk cellular proteins, as observed in cells carrying an ochre suppressor tRNA. Translational read‐through products generated from the crp gene in the presence of the antibiotics was efficiently tagged by the SsrA system, presumably because the ribosome reached the 3′ end of the mRNA defined by the terminator hairpin. The SsrA‐defective cells were more sensitive to the miscoding antibiotics compared to the wild‐type cells.Conclusion: We conclude that the SsrA system contributes to the survival of cells by dealing with translational errors in the presence of low concentrations of miscoding antibiotics.
The VAR1 locus of Arabidopsis encodes a chloroplastic FtsH and is responsible for leaf variegation in the mutant alleles
Authors: Sakamoto Wataru , Tamura Takayuki , Hanba‐Tomita Yuko ,   Sodmergen, Murata Minoru 
Published: March 2003

AbstractBackground: A leaf‐variegated mutation var1 of Arabidopsis results in the development of abnormal plastids and the formation of a green/white sector. Genetic analysis of the var1 mutant indicated that it acts synergistically with another mutation var2, suggesting that the two genes are relevant. The VAR2 locus has been shown to encode a chloroplastic FtsH, an ATP‐dependent protease which is possibly involved in the degradation of thylakoid proteins and plastid development.Results: In this study we show that the VAR1 locus encodes a chloroplastic FtsH protein homologous to VAR2. VAR1 contains a conserved motif for ATPase and a metalloprotease characteristic to FtsH proteins, and is targeted into chloroplasts. A VAR1‐fusion protein synthesized in vitro exhibited ATPase activity and partial metalloprotease activity. The maximum yield of photochemistry, measured by chlorophyll fluorescence, showed that the var1 mutants were sensitive to photoinhibitory light exposure at 800 µmol/m2/s.Conclusion: VAR1 and VAR2 comprise an FtsH small gene family together with other FtsH genes in Arabidopsis. VAR1 as well as VAR2 may play an important role in degrading photodamaged subunits in photosystem II. Loss of VAR1 and VAR2 perhaps impairs the photoprotection mechanism and thylakoid development, causing leaf variegation as a consequence.
Cyclin G1 associates with MDM2 and regulates accumulation and degradation of p53 protein
Authors: Kimura Shinya H. , Nojima Hiroshi 
Published: March 2003

AbstractBackground: Cyclin G1 is a transcriptional target of p53 and is induced by DNA damage in a p53 dependent manner. Analysis of cyclin G1 disrupted mice demonstrated that cyclin G1 is involved in many of the functions regulated by p53 such as apoptosis, growth control and check point regulation in response to DNA damage. The results suggest that the main role of cyclin G1 is to mediate or regulate the function of p53.Results: Western blot analysis revealed that the accumulation of p53 protein during the initial 24 h period following DNA damage is reduced in cyclin G1–/– cells compared to wild‐type cells. This decrease in p53 accumulation could be recovered by introducing a cDNA expressing cyclin G1. Cyclin G1 interacted directly with MDM2 and promoted the formation of the ARF/MDM2 complex within the initial 24 h period following DNA damage. Furthermore, 48 h after irradiation, accumulation of p53 protein was enhanced in cyclin G1–/– cells compared to wild‐type cells. In contrast, in 48 h postirradiated wild‐type cells, the cyclin G1‐MDM2 complex was found not to be associated with ARF but with the B′α subunit of protein phosphatase A.Conclusion: These results suggest that cyclin G1 stabilizes and promotes the degradation of p53 protein by associating, respectively, with MDM2 complexes containing ARF and PP2A.
Regulated protein–protein interaction between aPKC and PAR‐3 plays an essential role in the polarization of epithelial cells
Authors: Nagai‐Tamai Yoko , Mizuno Keiko , Hirose Tomonori , Suzuki Atsushi , Ohno Shigeo 
Published: March 2003

AbstractBackground: Recent studies have revealed that aPKC (atypical protein kinase C), PAR‐3 and PAR‐6 play indispensable roles in the regulation of various cell polarization events, from worms to mammals, suggesting that they comprise an evolutionarily conserved protein machinery which is essential for cell polarization. The three proteins interact with each other to form a ternary complex and thus mutually regulate their functionality and localization. Here, we investigated the biochemical nature of the aPKC–PAR‐3 interaction in detail to clarify its functional importance in cell polarity.Results: The highly conserved 26 amino acid sequence 816–841, in PAR‐3 was found to be necessary and sufficient for the tight association with aPKC. Among several conserved serine/threonine residues within the region, aPKC preferentially phosphorylates serine‐827 in vitro, and this phosphorylation reduces the stability of the PAR‐3–aPKC interaction. Several analyses using a phospho‐serine 827 specific antibody have established that this phosphorylation by aPKC occurs in vivo. Over‐expression of a point mutant of PAR‐3 (S827A), which is predicted to form a stable complex with aPKC, causes defects in the cell‐cell contact‐induced cell polarization of epithelial MDCK cells, similarly to a dominant negative mutant of aPKC.Conclusions: These results imply that serine 827 in the aPKC binding site of PAR‐3 is a target of aPKC and that the regulated interaction between a protein kinase, aPKC, and its substrate, PAR‐3, plays an essential role in the establishment of cell polarity.
Interaction of the chromatin compaction‐inducing domain (LR domain) of Ki‐67 antigen with HP1 proteins
Authors: Kametaka Ai , Takagi Masatoshi , Hayakawa Tomohiro , Haraguchi Tokuko , Hiraoka Yasushi , Yoneda Yoshihiro 
Published: March 2003

AbstractBackground: The LR domain of marsupial chmadrin is defined by its C‐terminal amino acid sequence, which contains several pairs of leucine (L) and arginine (R) residues. The LR domain of chmadrin causes a significant compaction of chromatin over the entire length of chromosomes when it is overproduced. The possible human homologue of chmadrin, Ki‐67 antigen (pKi‐67), also has a stretch of LR pairs, but with no obvious overall similarity, at its C‐terminus.Results: The LR domain of human pKi‐67 also induced chromatin compaction, both in human and marsupial cells. A yeast two‐hybrid assay and an in vitro binding assay demonstrated that the human LR domain binds to heterochromatin protein 1 (HP1), a well‐characterized molecule as a mediator of heterochromatin formation. In fixed cells stained with specific antibodies, the pKi‐67 was found to be co‐localized partially with HP1 at foci on chromosomes in an early G1 phase. Time‐lapse observation in living cells co‐expressing the fluorescently tagged proteins showed that the LR domain formed foci on chromosomes over a limited period of the cell cycle from the telophase to early G1 phase and that HP1 subsequently accumulated at these foci of the LR domain.Conclusions: Marsupial chmadrin and human pKi‐67 induce chromatin compaction across species, possibly via the interaction of its LR domain with HP1.
The upstream regulator, Rsr1p, and downstream effectors, Gic1p and Gic2p, of the Cdc42p small GTPase coordinately regulate initiation of budding in Saccharomyces cerevisiae
Authors: Kawasaki Ryosuke , Fujimura‐Kamada Konomi , Toi Hirofumi , Kato Hiroyuki , Tanaka Kazuma 
Published: March 2003

AbstractBackground: Cdc42p, a Rho family small GTPase, is essential for budding initiation in the yeast Saccharomyces cerevisiae. The homologous proteins Gic1p and Gic2p (Gic1/2p) are effectors of Cdc42p, but their precise functions remain unknown. Rsr1p/Bud1p is a Ras family small GTPase that controls the selection of the budding site. Previous observations suggested that Rsr1p‐GTP recruits Cdc24p, a GDP/GTP exchange factor for Cdc42p, at the incipient bud site. However, this model only addresses how Rsr1p determines the budding site, because the rsr1 mutant normally initiates budding.Results: Here we show that a rsr1 gic1 gic2 mutant fails to initiate budding, resulting in unbudded, large, and multinucleated cells. Expression of a dominant active or dominant negative mutant of RSR1 also inhibited the growth of the gic1 gic2 mutant, suggesting that cycling of Rsr1p between the GTP‐ and GDP‐bound forms is required for budding initiation in the gic1 gic2 mutant. Among the mutations in effectors of CDC42, only the gic1 gic2 mutation demonstrated a synthetic lethal interaction with rsr1. Increased gene dosage of CDC42 suppressed defects in budding initiation of rsr1 gic1 gic2 mutants containing additional mutations in other effectors of CDC42, including BNI1, CLA4 or STE20. The polarized localization of Bni1p‐GFP (green fluorescent protein) and Cla4p‐GFP was lost after depletion of Gic1p in the rsr1 gic2 mutant.Conclusion: We propose that Gic1/2p may stabilize or maintain a complex consisting of Cdc42p‐GTP and its effectors at the budding site, which are assembled by the action of the Rsr1p‐Cdc24p system.
Inversion for multiple parameter classes
Authors: Kennett B. L. N. , Sambridge M. 
Published: March 2003

Summary
Many geophysical data, such as the frequencies of the free oscillations of the Earth, depend on more than one type of model parameter. For inverse problems depending on multiple parameter classes, an iterative solution procedure is introduced in which each parameter class can be treated in the same way. This approach has considerable advantages where a large number of parameters are employed, but can still be useful for smaller systems.
The iteration by parameter class commences by solving for the direct dependence on a particular parameter class, and at subsequent iterations the cross-dependences between classes are introduced. The update affects only the right-hand side of the equations, and, because the same sets of equations have to be solved at each iteration, an efficient computational implementation can be made. The largest set of equations that has to be solved at a time corresponds to the number of variables in an individual parameter class rather than the full set of parameters, which confers substantial computational benefits for very large problems.
Interpreting non‐orthogonal split shear waves for seismic anisotropy in multicomponent VSPS
Authors: Li Xiang‐Yang , MacBeth Colin , Crampin Stuart 
Published: March 2003

There are two main sources of non‐orthogonality in multicomponent shear‐wave seismics: inherent non‐orthogonal split shear waves arising from substantial ray deviation in off‐symmetry planes due to strong anisotropy or complex overburden, and apparent non‐orthogonal split shear waves in the horizontal plane due to variation of the angle of incidence even if the two shear waves along the raypath are orthogonal. Many techniques for processing shear‐wave splitting in VSP data ignore these kinds of non‐orthogonality of the split shear waves.Assuming inherent non‐orthogonality in zero‐offset VSPs, and apparent non‐orthogonality in offset VSPs, we derive equations for the four‐component data matrix. These can be solved by extending the linear‐transform technique (LTT) to determine the shear‐wave polarizations in zero‐offset and offset VSPs. Both full‐wave synthetic and field data are used to evaluate the technique and to examine the effects of non‐orthogonal polarized split shear waves.If orthogonality is incorrectly assumed, errors in polarization measurements increase with the degree of non‐orthogonality, which introduces a consistent decreasing trend in the polarization measurements. However, the effect of non‐orthogonality on the estimation of geophone orientation and time delays of the two split shear waves is small and negligible in most realistic cases. Furthermore, for most cases of weak anisotropy (less than 5% shear‐wave anisotropy) apparent non‐orthogonality is more significant than inherent non‐orthogonality. Nevertheless, for strong anisotropy (more than 10% shear‐wave anisotropy) with complicated structure (tilted or inclined symmetry axis), inherent non‐orthogonality may no longer be negligible.Applications to both synthetic and real data show that the extended linear‐transform techniques permit accurate recovery of polarization measurements in the presence of both significant inherent and apparent non‐orthogonality where orthogonal techniques often fail.
GPR modelling by the Fourier method: improvement of the algorithm
Authors: Carcione  , Lenzi  , Valle  
Published: March 2003

We improve two aspects of the modelling scheme for the simulation of electromagnetic radio waves, based on the Fourier pseudospectral method.When there are large contrasts in the material properties, use of the standard algorithm (regular grid) causes a series of artefacts, as, for instance, ringing and acausal events. These problems, due to the non‐locality of the differential operator, are solved by using the staggered Fourier method (staggered grid).Realistic radiation patterns can be obtained from simple combinations of magnetic and electric sources. If the directivity pattern of the antenna is known, from either a finite‐difference simulation or an analytic evaluation or an experimental characterization, it can then be simulated by a composite‐source concept. This effective source is implemented in the modelling algorithm by means of a perturbation technique, which first computes the intensity and directional spectra of the single electromagnetic sources. Their location is optimized to obtain the best fit with a minimum number of sources. The approach is, in principle, valid for the far‐field radiation pattern of the antenna.
Marine seismic wavefield measurement to remove sea‐surface multiples
Authors: Ziolkowski  , Taylor  , Johnston  
Published: March 2003

We propose a new method for removing sea‐surface multiples from marine seismic reflection data in which, in essence, the reflection response of the earth, referred to a plane just above the sea‐floor, is computed as the ratio of the plane‐wave components of the upgoing wave and the downgoing wave. Using source measurements of the wavefield made during data acquisition, three problems associated with earlier work are solved: (i) the method accommodates source arrays, rather than point sources; (ii) the incident field is removed without simultaneously removing part of the scattered field; and (iii) the minimum‐energy criterion to find a wavelet is eliminated.Pressure measurements are made in a horizontal plane in the water. The source can be a conventional array of airguns, but must have both in‐line and cross‐line symmetry, and its wavefield must be measured and be repeatable from shot to shot. The problem is formulated for multiple shots in a two‐dimensional configuration for each receiver, and for multiple receivers in a two‐dimensional configuration for each shot. The scattered field is obtained from the measurements by subtracting the incident field, known from measurements at the source. The scattered field response to a single incident plane wave at a single receiver is obtained by transforming the common‐receiver gather to the frequency–wavenumber domain, and a single component of this response is obtained by Fourier transforming over all receiver coordinates. Each scattered field component is separated into an upgoing wave and a downgoing wave using the zero‐pressure condition at the water‐surface. The upgoing wave may then be expressed as a reflection coefficient multiplied by the incident downgoing wave plus a sum of scattered downgoing plane waves, each multiplied by the corresponding reflection coefficient. Keeping the upgoing scattered wave fixed, and using all possible incident plane waves for a given frequency, yields a set of linear simultaneous equations for the reflection coefficients which are solved for each plane wave and for each frequency. To create the shot records that would have been measured if the sea‐surface had been absent, each reflection coefficient is multiplied by complex amplitude and phase factors, for source and receiver terms, before the five‐dimensional Fourier transformation back to the space–time domain.