bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cleavage reaction of HDV ribozymes in the presence of Mg2+ is accompanied by a conformational change
Authors: Tanaka Yoichiro , Tagaya Mitsuhiro , Hori Tamaki , Sakamoto Taiichi , Kurihara Yasuyuki , Katahira Masato , Uesugi Seiichi 
Published: March 2003

AbstractBackground: Hepatitis delta virus (HDV) ribozymes cleave RNA in the presence of divalent metal ions. We have previously elucidated the solution conformation of a minimized trans‐acting HDV ribozyme and obtained evidence by NMR study that an Mg2+ ion binds to a site close to the cleavage site.Results: We examined two ribozyme systems: a pre‐cleavage complex with a non‐cleavable substrate analogue (mS8) and a post‐cleavage complex with a 3′ cleavage product (P7). Upon titration with MgCl2, the complex with P7 showed a profound spectral change, while that with mS8 showed broadening of the signals. Analysis of the NOESY spectra of the P7 complex at high Mg2+ concentration revealed that a G:U pair is formed within the L3 loop, and the P1 and P4 stems are stabilized with respect to those of the pre‐cleavage complex.Conclusion: The present analysis indicates that the cleavage reaction of the HDV ribozyme produces a big conformational change. Furthermore, presence of the 5′‐terminal cytidine residue prevents this conformational change and its absence stabilizes the product–ribozyme complex in the presence of Mg2+. The structure of the Mg2+‐bound P7 complex is similar to the crystal structure found for a product–ribozyme complex but is different from the pre‐cleavage structure.
Over‐expression of human DNA polymerase lambda in E. coli and characterization of the recombinant enzyme
Authors: Shimazaki Noriko , Yoshida Kenta , Kobayashi Toshiko , Toji Shingo , Tamai Katsuyuki , Koiwai Osamu 
Published: March 2003

AbstractBackground: DNA polymerase lambda (Pol λ) was recently identified as a new member of the family X of DNA polymerases in eukaryotic cells. Pol λ contains a nuclear localization signal (NLS), a BRCA1‐C terminal (BRCT) domain, a proline‐rich region, helix‐hairpin‐helix (HhH) and pol X motifs. Since the amino acid sequence for Pol λ shares a high degree of homology to Pol β, Pol λ is considered to have a similar enzymatic nature to Pol β.Results: Recombinant human Pol λ was shown to possess template‐directed DNA polymerase activity in its monomeric form. Pol λ required either Mn2+ or Mg2+ as a metal co‐factor to catalyse this activity, and optimal activity was detected at pH 8.5–9.0. Pol λ was insensitive to aphidicolin, but was sensitive to dideoxynucleoside triphosphates or N‐ethylmaleimide. By constructing the truncated Pol λ, the proline rich region was shown to act in a suppression of its polymerization activity. A chimeric enzyme comprised of the Pol λ N‐terminal region and Pol β also showed a reduced Pol β activity. Proliferating cell nuclear antigen (PCNA) directly interacts with Pol λ through its Pol β like region in vitro.Conclusions: Pol λ possesses similar enzymatic nature to Pol β; requirements of cations and optimal conditions for pH and NaCl concentration, aside from sensitivity to N‐ethylmaleimide and template preference. The proline rich region of Pol λ functions as a suppressor domain for its polymerization activity (SDPA). Pol λ interacts directly with PCNA through its Pol β like region. The functional consequence of this interaction is the negative regulation of Pol λ activity.
Characterization of the chicken L‐Maf, MafB and c‐Maf in crystallin gene regulation and lens differentiation
Authors: Yoshida Tomonori , Yasuda Kunio 
Published: March 2003

AbstractBackground: Members of the Maf family, including L‐Maf, MafB and c‐Maf, are ‘basic region/leucine zipper’ (bZIP) transcription factors. Maf proteins contain a highly conserved acidic transactivation domain (AD), and a bZIP region that mediates DNA‐binding activity. The hinge region between AD and bZIP varies considerably in length between different proteins. Recent studies reveal that L‐Maf, c‐Maf and MafB play key roles in vertebrate lens development.Results: We investigated the transactivation activity of individual factors in culture cells to analyse their specific functions. In transient transfection assays with a reporter gene containing Maf responsive elements, MafB and c‐Maf activated higher levels of the reporter gene than L‐Maf. However, L‐Maf transactivated the αA‐crystallin promoter as effectively as MafB and c‐Maf, and induced the expression of the endogenous δ‐crystallin gene more efficiently than the other two proteins. Domain‐swapping experiments reveal that the bZIP region of MafB takes part in strong transcriptional activity, while the acidic and hinge regions (AH) of c‐Maf collectively serve as a strong transactivation domain. The AH region of L‐Maf (but not c‐Maf) conferred transactivation activity to induce δ‐crystallin gene expression.Conclusions: These results suggest that despite their similar DNA binding properties, L‐Maf, MafB and c‐Maf regulate different sets of target genes by complex interactions with multiple factors that recognize cis‐elements in promoters. The AH region of L‐Maf has a distinct role in inducing endogenous δ‐crystallin gene.
Targeted elimination of the follicular label‐retaining cells by photo‐induced cell killing caused a defect on follicular renewal on mice
Authors: Kameda Takashi , Hatakeyama Shin , Ma Ying‐Zhe , Kawarada Yoshihiko , Kawamata Makiko , Terada Kunihiko , Sugiyama Toshihiro 
Published: March 2003

AbstractBackground: One of the most well‐known ways to identify stem cells is to search for the slow‐cycling cells (label‐retaining cells; LRCs), by labelling their DNA. The bulge of hair follicle is assumed to identify the location of the follicular stem cells. While this assumption was supported by previous analyses of cell tracing, it is still not clear whether the LRCs are critical for follicular renewal.Results: To solve this problem, we tried to selectively eliminate the bromodeoxyuridine (BrdU)‐labelled follicular LRCs by a photo‐induced cell killing method, in combination with Hoechst 33258 treatment. We labelled the slow‐cycling cells in the follicular bulge by repeated administration of the BrdU, followed by a chase period. When the labelled mice skin was irradiated at the telogen phase after the Hoechst 33258 treatment, we observed apoptotic cells in the bulge area 18 h after the irradiation and a defect on the follicular renewal at the next anagen phase. The time course of appearance of hair defect suggests that only the late telogen follicle is sensitive to irradiation.Conclusions: This finding suggests that the LRCs contribute to the renewal of the hair follicle, and they might proliferate at a restricted point in the hair cycle to supply hair germinative cells as previously predicted.
Zebrafish DAZ‐like protein controls translation via the sequence ‘GUUC’
Authors: Maegawa Shingo , Yamashita Masakane , Yasuda Kunio , Inoue Kunio 
Published: March 2003

AbstractBackground: In many species, DAZ homologous genes encode RNA‐binding proteins containing two conserved motifs, namely the RNA‐recognition motif (RRM) and the DAZ motif. Genetic analysis and gene disruption studies have demonstrated that DAZ family proteins play important roles in gametogenesis. However, little is known about the biochemical functions of DAZ family proteins.Results: Using in vitro selection and UV‐crosslinking experiments, we identified the sequence ‘GUUC’ as the target RNA sequence of zebrafish DAZ‐like protein (zDAZL). In transfection experiments, zDAZL protein activated translation in a manner dependent on the binding sequence in the 3′UTR of the Drosophila twine gene or zDazl gene. Moreover, it is highly likely that the zDAZL protein associates with polysomes through the DAZ motif in vivo, and that the association with polysomes is indispensable for translational activation.Conclusions: This is the first report that the DAZ family protein directly promotes the translation of the target mRNAs in vertebrates. This study provides important insights into the molecular mechanisms underlying the post‐transcriptional regulation of DAZ family proteins in gametogenesis.
Naso‐maxillary deformity due to frontonasal expression of human transthyretin gene in transgenic mice
Authors: Noguchi Hiromitsu , Kaname Tadashi , Sekimoto Tomohisa , Senba Kei , Nagata Yasushi , Araki Masatake , Abe Makoto , Nakagata Naomi , Ono Tomomichi , Yamamura Ken‐ichi , Araki Kimi 
Published: March 2003

AbstractBackground Retinoic acid, a metabolic product of retinol, is essential for craniofacial morphogenesis. Transthyretin (TTR) is a plasma protein delivering retinol to tissues. We produced several transgenic mouse lines using the human mutant TTR (hTTRMet30) gene to establish a mouse model of familial amyloidotic polyneuropathy. One of the lines showed an autosomal dominant inheritance of naso‐maxillary deformity termed Nax.Results: The Nax malformation was characterized by a hypoplastic developmental defect of the frontonasal region. Homozygous mice with higher transgene expressions showed more severe phenotypes, but a subline, in which the copy number and expression of the transgene was reduced, showed a normal phenotype, indicating that the hTTRMet30 expression caused the malformation. Nax mice began to express the hTTRMet30 gene in the nasal placode from embryonic day 10.5 (E10.5), which was 2 days earlier than in the other transgenic lines with a normal phenotype. Excessive cell death was observed in the nasal placode of the E10.5 Nax embryos. In addition, the forced expression of hTTRMet30 in the nasal placode of transgenic mice resulted in similar phenotypes.Conclusion: The expression of the hTTRMet30 gene in the nasal placode at E10.5 induced apoptotic cell death, leading to hypoplastic deformity in the frontonasal region.
Simultaneous acceleration of the cell cycle and suppression of apoptosis by splice variant delta‐6 of the candidate tumour suppressor LUCA‐15/RBM5
Authors: Mourtada‐Maarabouni Mirna , Sutherland Leslie C. , Meredith Janet M. , Williams Gwyn T. 
Published: March 2003

AbstractBackground: The short arm of chromosome 3 is thought to include one or more tumour suppressor genes (TSGs), since carcinoma of various tissues display deletions in this region. Many genes mapping to this region have recently been identified, including the LUCA‐15/RBM5 gene.Results: In this study we report the cloning from human bone marrow library of a splice variant of LUCA‐15 which lacks exon 6, resulting in a frameshift and producing a truncated protein of 150 amino acids instead of 815 amino acids. This variant is widely expressed at a low level in normal tissues and is expressed at increased levels in T‐leukaemic cell lines. Over‐expression of this splice variant after electroporation both shortened the cell cycle and inhibited CD95‐mediated apoptosis in CEM‐C7 T‐cells. In marked contrast, over‐expression of the full length LUCA‐15/RBM5 suppressed cell proliferation both by inducing apoptosis and by extending the G1 phase of the cell cycle.Conclusion: These results, taken together with previous observations from ourselves and others, suggest that LUCA‐15 is involved in the control of both apoptosis and the cell cycle. Since oncogenesis often relies on separate changes in molecules regulating apoptosis on the one hand, and proliferation, on the other, the discovery of a candidate tumour suppressor gene which affects both processes simultaneously is likely to be of major significance.
Overproduction of a conserved domain of fission yeast and mammalian translation initiation factor eIF4G causes aberrant cell morphology and results in disruption of the localization of F‐actin and the organization of microtubules
Authors: Hashemzadeh‐Bonehi Lida , Curtis Penelope S. , Morley Simon J. , Thorpe Julian R. , Pain Virginia M. 
Published: March 2003

AbstractBackground: The recruitment of mRNA for translation involves the assembly at the 5′cap of a complex of three initiation factors: the cap binding protein eIF4E, the ATP‐dependent RNA helicase eIF4A and the scaffold protein eIF4G. eIF4G mediates the binding of this mRNA–protein complex to the 43S ribosomal preinitiation complex. There is growing recognition that the components of the translational apparatus interact functionally with cytoskeletal components. Here we report specific effects of the over‐expression of human and fission yeast eIF4G domains on cell morphology in Schizosaccharomyces pombe.Results: A single gene encoding fission yeast eIF4G was identified and demonstrated to be essential. We have over‐expressed fragments corresponding to the conserved functional domains of eIF4G. At expression levels that did not disrupt rates of overall translation or protein accumulation, a fragment of S. pombe eIF4G, 4G‐NOB, corresponding to the minimal region of human eIF4G required to support cap‐independent mRNA recruitment, was found to impair cell proliferation in fission yeast. This resulted from defects in cytokinesis, and was associated with the disruption of both microtubules and actin microfilaments. The over‐expressed fragment was itself localized to the cell ends, the nuclear periphery and the septum.Conclusions: This is the first demonstration of a link between a translation initiation factor and mechanisms controlling cell morphology. The data suggest a direct or indirect interaction between the functional domains of eIF4G and cellular structures involved in cytokinesis.
Geophysical inversion with a neighbourhood algorithm—I. Searching a parameter space
Authors: Sambridge Malcolm 
Published: March 2003

SummaryThis paper presents a new derivative-free search method for finding models of acceptable data fit in a multidimensional parameter space. It falls into the same class of method as simulated annealing and genetic algorithms, which are commonly used for global optimization problems. The objective here is to find an ensemble of models that preferentially sample the good data-fitting regions of parameter space, rather than seeking a single optimal model. (A related paper deals with the quantitative appraisal of the ensemble.)The new search algorithm makes use of the geometrical constructs known as Voronoi cells to derive the search in parameter space. These are nearest neighbour regions defined under a suitable distance norm. The algorithm is conceptually simple, requires just two ‘tuning parameters’, and makes use of only the rank of a data fit criterion rather than the numerical value. In this way all difficulties associated with the scaling of a data misfit function are avoided, and any combination of data fit criteria can be used. It is also shown how Voronoi cells can be used to enhance any existing direct search algorithm, by intermittently replacing the forward modelling calculations with nearest neighbour calculations.The new direct search algorithm is illustrated with an application to a synthetic problem involving the inversion of receiver functions for crustal seismic structure. This is known to be a non-linear problem, where linearized inversion techniques suffer from a strong dependence on the starting solution. It is shown that the new algorithm produces a sophisticated type of ‘self-adaptive’ search behaviour, which to our knowledge has not been demonstrated in any previous technique of this kind.
Local Bayesian inversion: theoretical developments
Authors: Moraes Fernando S. , Scales John A. 
Published: March 2003

SummaryWe derive a new Bayesian formulation for the discrete geophysical inverse problem that can significantly reduce the cost of the computations. The Bayesian approach focuses on obtaining a probability distribution (the posterior distribution), assimilating three kinds of information: physical theories (data modelling), observations (data measurements) and prior information on models. Once this goal is achieved, all inferences can be obtained from the posterior by computing statistics relative to individual parameters (e.g. marginal distributions), a daunting computational problem in high dimensions.Our formulation is developed from the working hypothesis that the local (subsurface) prior information on model parameters supercedes any additional information from other parts of the model. Based on this hypothesis, we propose an approximation that permits a reduction of the dimensionality involved in the calculations via marginalization of the probability distributions. The marginalization facilitates the tasks of incorporating diverse prior information and conducting inferences on individual parameters, because the final result is a collection of 1-D posterior distributions. Parameters are considered individually, one at a time. The approximation involves throwing away, at each step, cross-moment information of order higher than two, while preserving all marginal information about the parameter being estimated. The main advantage of the method is allowing for systematic integration of prior information while maintaining practical feasibility. This is achieved by combining (1) probability density estimation methods to derive marginal prior distributions from available local information, and (2) the use of multidimensional Gaussian distributions, which can be marginalized in closed form.Using a six-parameter problem, we illustrate how the proposed methodology works. In the example, the marginal prior distributions are derived from the application of the principle of maximum entropy, which allows one to solve the entire problem analytically. Both random and modelling errors are considered. The uncertainty measure for estimated parameters is provided by 95 per cent probability intervals calculated from the marginal posterior distributions.
Automatic cross‐well tomography by semblance and differential semblance optimization: theory and gradient computation
Authors: Plessix R.‐E. , Mulder W.A. , Kroode A.P.E. ten 
Published: March 2003

A technique for automatic cross‐well tomography based on semblance and differential semblance optimization is presented. Given a background velocity, the recorded seismic data traces are back‐propagated towards the source, i.e. shifted towards time zero using the modelled traveltime between the source and the receiver and corrected for the geometrical spreading. Therefore each back‐propagated trace should be a pulse, close to time zero. The mismatches between the back‐propagated traces indicate an error in the velocity model. This error can be measured by stacking the back‐propagated traces (semblance optimization) or by computing the norm of the difference between adjacent traces (differential semblance optimization).It is known from surface seismic reflection tomography that both the semblance and differential semblance functional have good convexity properties, although the differential semblance functional is believed to have a larger basin of attraction (region of convergence) around the true velocity model. In the case of the cross‐well transmission tomography described in this paper, similar properties are found for these functionals.The implementation of this automatic method for cross‐well tomography is based on the high‐frequency approximation to wave propagation. The wavefronts are constructed using a ray‐tracing algorithm. The gradient of the cost function is computed by the adjoint‐state technique, which has the same complexity as the computation of the functional. This provides an efficient algorithm to invert cross‐well data. The method is applied to a synthetic data set to demonstrate its efficacy.
Detection of potential fields source boundaries by enhanced horizontal derivative method
Authors: Fedi M. , Florio G. 
Published: March 2003

A high‐resolution method to image the horizontal boundaries of gravity and magnetic sources is presented (the enhanced horizontal derivative (EHD) method). The EHD is formed by taking the horizontal derivative of a sum of vertical derivatives of increasing order. The location of EHD maxima is used to outline the source boundaries. While for gravity anomalies the method can be applied immediately, magnetic anomalies should be previously reduced to the pole. We found that working on reduced‐to‐the‐pole magnetic anomalies leads to better results than those obtainable by working on magnetic anomalies in dipolar form, even when the magnetization direction parameters are not well estimated. This is confirmed also for other popular methods used to estimate the horizontal location of potential fields source boundaries.The EHD method is highly flexible, and different conditions of signal‐to‐noise ratios and depths‐to‐source can be treated by an appropriate selection of the terms of the summation. A strategy to perform high‐order vertical derivatives is also suggested. This involves both frequency‐ and space‐domain transformations and gives more stable results than the usual Fourier method.The high resolution of the EHD method is demonstrated on a number of synthetic gravity and magnetic fields due to isolated as well as to interfering deep‐seated prismatic sources. The resolving power of this method was tested also by comparing the results with those obtained by another high‐resolution method based on the analytic signal. The success of the EHD method in the definition of the source boundary is due to the fact that it conveys efficiently all the different boundary information contained in any single term of the sum.Application to a magnetic data set of a volcanic area in southern Italy helped to define the probable boundaries of a calderic collapse, marked by a number of magmatic intrusions. Previous interpretations of gravity and magnetic fields suggested a subcircular shape for this caldera, the boundaries of which are imaged with better detail using the EHD method.