bluuebunny/crossref_metadata_2025_split huggingface dataset:
Somatic mutations of synaptic cadherin (CNR family) transcripts in the nervous system
Authors: Hirayama Teruyoshi , Sugino Hidehiko , Yagi Takeshi 
Published: March 2003

BackgroundCadherin‐related neuronal receptor (CNR) family genes have been identified in the nervous system by screening molecules bound to Fyn‐tyrosine kinase. The CNR family is comprised of diverse synaptic cadherins. The genomic organization of the CNR genes, composed of variable and constant regions, is similar to that of the immunoglobulin gene cluster. The nervous system is characterized by the acquisition of diverse function. This feature is similar to the immune system. In the immune system, the generation and selection of immunoglobulin gene mutants is the underlying basis for acquired immunity. We therefore examined somatic regulation of the CNR family genes in the nervous system to determine whether a similar mechanism controls nervous system development.ResultsWe first demonstrated that approximately 10% of the CNR3 transcripts were trans‐transcripts between the variable and constant exons at the adult stage. Furthermore, somatic mutations of CNR3 transcripts accumulated during brain development, with a marked bias for A‐to‐G and U‐to‐C transitions. Approximately 70% of the CNR3 transcripts exhibited a mutation characterized by the addition of a CU‐repeat; these transcripts contained seven continuous CU‐repeats in the 3′ untranslated region at the adult stage, whereas the CNR genomic DNA contained six continuous CU‐repeats. Interestingly, a high rate of replacement mutations was detected in the first cadherin domain that functions in acquisition of specificity for cell adhesion in cadherins, while in the other regions the occurrence of silent mutations increased during development.ConclusionThe present report is the first description of the generation and possible selection of somatic mutations of synaptic cadherin transcripts. The somatic alterations of CNR family transcripts and their synaptic localization have interesting implications for the molecular basis underlying the establishment of somatic rearrangement of neuronal networks.
TBP‐interacting protein TIP120A is a new global transcription activator with bipartite functional domains
Authors: Kayukawa Kentaro , Kitajima Yoko , Tamura Taka‐aki 
Published: March 2003

BackgroundWe previously identified a TBP (TATA‐binding protein)‐interacting protein 120A (TIP120A) from rat liver nuclear extracts. TIP120A is thought to be a unique global transcription factor that can interact with TBP and can stimulate all classes of eukaryotic transcription.ResultsWe produced various truncation proteins of TIP120A to delineate its functional domains. TIP120A binds to TBP in the acidic amino acid‐rich N‐terminal region and in the leucine‐rich C‐terminal region. These regions exhibited an ability to stimulate basal transcription in vitro. In addition, these two regions overlap with domains that facilitate nonspecific DNA‐binding of RNA polymerase II. The sequences of these two regions are significantly conserved among TIP120A homologues of eukaryotes.ConclusionsTIP120A is a bipartite transcription factor, and both N‐terminal and C‐terminal regions exhibit TBP‐binding activity and stimulate the basal transcription ability.
Defective development of secretory neurones in the hypothalamus of Arnt2‐knockout mice
Authors: Hosoya Tomonori , Oda Yoshihito , Takahashi Satoru , Morita Masanobu , Kawauchi Shimako , Ema Masatsugu , Yamamoto Masayuki , Fujii‐Kuriyama Yoshiaki 
Published: March 2003

BackgroundWithin the basic region‐helix‐loop‐helix (bHLH)‐PAS family of transcription factors, Arnt and Arnt2 play unique roles; these two factors not only heterodimerize with themselves, but also with other members of this family and they act as transcription regulators which bind to specific DNA elements. Whereas Arnt is broadly expressed in various tissues, the expression of Arnt2 is known to be limited to the neural tissues.ResultsTo elucidate the function of Arnt2 in detail, we cloned the mouse Arnt2 gene and its gene structure was determined. We subsequently generated germ line Arnt2 mutant mice by gene targeting technology. Heterozygous Arnt2 mice were viable, but homozygous Arnt2 gene knockout mice died shortly after birth. Histological and immunological analyses revealed that the supraoptic nuclei (SON) and the paraventricular nuclei (PVN) are hypocellular. Moreover, secretory neurones identified by the expression of neurosecretory hormone such as arginine vasopressin, oxytocin, corticotrophin‐releasing hormone and somatostatin are completely absent in SON and PVN in the mutant Arnt2 mice. Consistent with these observations, prospective SON and PVN neurones which express Brn2 appeared around E13.5 in the mantle zone, but no neurones which expressed the neurosecretory hormones were found in the SON and PVN regions.ConclusionsThese data show that the transcription factor Arnt2 controls the development of the secretory neurones at the later or final stages of differentiation rather than at the beginning stage. Strikingly similar observations have been reported with the Sim1 deficient mice. Taken together, our results demonstrate that Arnt2 is an indispensable transcription factor for the development of the hypothalamus, and suggest that Arnt2 is an obligatory partner molecule of Sim1 in the developmental process of the neuroendocrinological cell lineages.
Requirement of Syk‐phospholipase C‐γ2 pathway for phorbol ester‐induced phospholipase D activation in DT40 cells
Authors: Hitomi Tomohiro , Yanagi Shigeru , Inatome Ryoko , Ding Junyi , Takano Tomoko , Yamamura Hirohei 
Published: March 2003

BackgroundTreatment of many cell types with phorbol esters stimulates phospholipase D (PLD) activity implying regulation of the enzyme by protein kinase C. Studies of the effects of several protein‐tyrosine kinase (PTK) inhibitors have suggested that PTK(s) play some roles in the phorbol ester‐induced PLD activation, but it remains unclear how and which PTK(s) is involved in this pathway. In this study, we investigated the roles of Syk and other PTKs for the phorbol esters, 12‐O‐tetradecanoylphorbol 13‐acetate (TPA)‐induced PLD activation in K562 and DT40 cells.ResultsTPA‐induced PLD activation was remarkably reduced in both Syk dominant negative mutant K562 cells and Syk deficient DT40 B cells. Mutational analysis further indicated that two major autophosphorylation sites (Tyr‐518 and Tyr‐519) of Syk are critical for PLD activation. Similarly, TPA‐induced PLD activation was reduced in Btk deficient cells, but unaffected in Lyn deficient cells. Finally, in cells deficient in the PLC‐γ2, one of the phosphorylated substrates regulated by Syk and Btk, TPA‐induced PLD activation, as well as phosphatidylinositol 4,5‐bisphosphate (PIP2) hydrolysis was remarkably reduced.ConclusionsWe demonstrated that the Syk, Btk and PLC‐γ2 pathways are required for TPA‐induced PLD activation in DT40 cells.
PAR‐6 regulates aPKC activity in a novel way and mediates cell‐cell contact‐induced formation of the epithelial junctional complex
Authors: Yamanaka Tomoyuki , Horikoshi Yosuke , Suzuki Atsushi , Sugiyama Yuki , Kitamura Koichi , Maniwa Rika , Nagai Yoko , Yamashita Akio , Hirose Tomonori , Ishikawa Hiroko , Ohno Shigeo 
Published: March 2003

Background PAR‐6, aPKC and PAR‐3 are polarity proteins that co‐operate in the establishment of cell polarity in Caenorhabditis elegans and Drosophila embryos. We have recently shown that mammalian aPKC is required for the formation of the epithelia‐specific cell‐cell junctional structure. We have also revealed that a mammalian PAR‐6 forms a ternary complex with aPKC and ASIP/PAR‐3, and localizes at the most apical end of the junctional complex in epithelial cells.Results The ternary complex formation and junctional co‐localization of PAR‐6 with aPKC and ASIP/PAR‐3 are observed during the early stage of epithelial cell polarization. In addition, over‐expression of the PAR‐6 mutant with CRIB/PDZ domain in MDCK cells disturbs the cell‐cell contact‐induced junctional localization of tight junction proteins, as well as inhibiting TER development. Furthermore, the binding of Cdc42:GTP to the CRIB/PDZ domain of PAR‐6 enhances the kinase activity of PAR‐6‐bound aPKC. Detailed analyses suggest that the binding of PAR‐6 to aPKC has the intrinsic potential to activate aPKC, which is only released when Cdc42:GTP binds to the CRIB/PDZ domain.Conclusion The results indicate the involvement of PAR‐6 in the aPKC function which is required for the cell‐cell adhesion‐induced formation of epithelial junctional structures, possibly through the cooperative regulation of aPKC activity with Cdc42.
Reconstitution of recombinant TFIIH that can mediate activator‐dependent transcription
Authors: Fukuda Aya , Yamauchi Jun , Wu Shwu‐Yuan , Chiang Cheng‐Ming , Muramatsu Masami , Hisatake Koji 
Published: March 2003

Background TFIIH is one of the general transcription factors required for accurate transcription of protein‐coding genes by RNA polymerase II. TFIIH has helicase and kinase activities, plays a role in promoter opening and promoter escape, and is also implicated in efficient activator‐dependent transcription.Results We have established a reconstitution system of recombinant TFIIH using a three‐virus baculovirus expression system. The recombinant TFIIH was active in CTD kinase and DNA helicase assays, and showed both basal and activator‐dependent transcriptional activities that were indistinguishable from those of HeLa cell‐derived TFIIH. Further analyses using recombinant TFIIH confirmed a critical role of TFIIH in activator‐dependent transcription. The dose response of TFIIH in activator‐dependent transcription suggested that mere recruitment of TFIIH is not sufficient for transcriptional activation. The sensitivity of activator‐dependent transcription to nonhydrolysable ATP analogues indicated the importance of the enzymatic activities of TFIIH in transcriptional activation.Conclusions Our results raise a possibility that transcriptional activation by GAL4‐VP16 requires enzymatic activities. Recombinant TFIIH reconstituted from this baculovirus system should be useful for analysis of the mechanisms of activation by GAL4‐VP16.
The mouse Snrpn minimal promoter and its human orthologue: activity and imprinting
Authors: Hershko Alon Y. , Finberg Yael , Kantor Boris , Shemer Ruth , Razin Aharon 
Published: March 2003

Background Microdeletions in chromosome 15q13‐15 of Prader‐Willi (PWS) and Angelman Syndrome (AS) patients suggested that SNRPN promoter/exon 1, together with a short sequence located approximately 35 kb upstream, constitute an imprinting control centre that regulates the entire 2 Mb PWS/AS imprinted domain. We have recently shown that a minitransgene composed of the human upstream sequence and mouse Snrpn promoter/exon 1 harbours all the elements necessary for establishing and maintaining an imprinted state.Results Here we describe, using transfection experiments, the Snrpn minimal promoter (SMP), being composed of the entire 76 bp exon 1 and 84 bp of upstream sequence. A 7 bp element (SBE) within SMP that, in its unmethylated state binds a specific protein, is absolutely required for promoter activity. The orthologous human sequence, in spite of the fact that it possesses an identical SBE, failed to display promoter activity in transfection experiments and failed to create a methylated state of the maternal allele. Transgenic experiments reveal that a mutation in SBE of the mouse sequence did not completely abolish methylation of the maternal allele, indicating that sequences outside SBE participate in this process. Replacement of human exon 1 with the mouse orthologue replenished promoter activity, but left the maternal allele in the transgenic experiment unmethylated. The reciprocal chimera, in which mouse exon 1 was replaced by the human orthologue resulted in loss of promoter activity and did not support differential methylation.Conclusions The observations made by in vitro and in vivo experiments suggest that several cis elements which are involved in Snrpn promoter activity and the imprinting process are present in the mouse promoter and absent in the human orthologous sequence.
Herpes simplex virus encodes a virion‐associated protein which promotes long cellular processes in over‐expressing cells
Authors: Takakuwa Hiroki , Goshima Fumi , Koshizuka Tetsuo , Murata Takayuki , Daikoku Tohru , Nishiyama Yukihiro 
Published: March 2003

Background Herpes simplex virus (HSV) possesses a number of accessory genes which are dispensable for replication in cell culture. A previous study showed that the UL21 gene product of HSV type 1 is a virion component that is not necessary for viral replication. The function of the gene product remains unknown.Results We found that the HSV‐1 UL21 gene product, a capsid‐associated tegument protein with an apparent molecular mass of 62 kDa, promotes the outgrowth of long cellular processes when it is over‐expressed in non‐neural cells. The UL21 protein co‐localizes and physically associates with microtubules in the long processes. Analysis using mutant proteins implicates a proline‐rich region in promotion of the processes.Conclusions The results suggest that the UL21 protein, like tau and other MAPs, promotes the process by directly or indirectly interacting with microtubules and facilitates the intracellular transport of the virus.
Transgenic over‐expression of MafK suppresses T cell proliferation and function in vivo
Authors: Yoh Keigyou , Sugawara Takehiko , Motohashi Hozumi , Takahama Yousuke , Koyama Akio , Yamamoto Masayuki , Takahashi Satoru 
Published: March 2003

Background The small Maf proteins regulate gene transcription from Maf recognition elements (MARE). These proteins do not contain a canonical transactivation domain. Depending upon the ratio of small Maf proteins to their partner proteins, which either possess a transactivation domain or not, transcription can be switched on or off.Results Transgenic mice were generated which over‐express the small Maf family member MafK, specifically in the T cell lineage. It was our expectation that the high level of MafK would shift the balance to the formation of MafK homodimer and thereby repress MARE‐dependent transcription. The transgenic mice had a shortened life span because of Pneumocystis carinii pneumonia and displayed a decrease in thymocytes and lower IL‐2 and IL‐4 mRNA expression levels. Analyses by electrophoretic gel mobility shift assay revealed that over‐expressed MafK could interact with the proximal AP‐1 sequence of IL‐2 and the MARE in the IL‐4 promoter region.Conclusion These results indicate that when over‐expressed, MafK binds to a MARE‐like sequence and represses MARE‐dependent transcription. Consequently, T cell proliferation and cytokine secretion are affected. The MafK homodimer serves as an important molecular probe for evaluating the role played by cis‐acting MAREs in the proliferation and function of T cells.
Fission yeast chk1 mutants show distinct responses to different types of DNA damaging treatments
Authors: Francesconi Stefania , Smeets Monique , Grenon Muriel , Tillit Jeanne , Blaisonneau Joël , Baldacci Giuseppe 
Published: March 2003

AbstractBackground: Chk1 kinase is activated by phosphorylation at serine‐345 by Rad3 checkpoint kinase and is required for DNA damage checkpoint in late S and G2 phase of S. pombe cell cycle. We studied the ability of two chk1 mutants, chk1‐1 and chk1‐2, to undergo phosphorylation and to delay cell cycle progression in response to different types of DNA lesions.Results: Both the Chk1‐1 and Chk1‐2 mutant proteins are phosphorylated to various extents when DNA is damaged in early G2 phase of cell cycle by either UV irradiation or gamma irradiation. However, chk1‐2 mutant does not delay cell cycle progression in a dose dependent manner specifically upon gamma irradiations. This defect is not associated with an important loss of survival. Furthermore, both chk1 mutants survive to Camptothecin treatment despite undetectable Chk1‐1 or Chk1‐2 phosphorylated forms. We show that both mutant proteins are not phosphorylated in cds1 devoid cells treated with ribonucleotide reductase inhibitor hydroxyurea or when the replisome is affected by a thermosensitive mutation in DNA polymerase δ. This inability is associated with the loss of checkpoint function. We found that an increased level of Crb2/Rhp9 protein specifically complements the defect of the chk1‐1 mutant allowing Chk1‐1 phosphorylation upon treatment with hydroxyurea of dcds1 cells.Conclusions: Mutants chk1‐1 and chk1‐2 behave differently according to the type of lesion generated on DNA.
The SH3, HOOK and guanylate kinase‐like domains of hDLG are important for its cytoplasmic localization
Authors: Kohu Kazuyoshi , Ogawa Fumiaki , Akiyama Tetsu 
Published: March 2003

AbstractBackground: hDLG, the human homologue of the Drosophila tumour suppressor dlg, functions as a scaffolding protein that facilitates the transmission of diverse downstream signals. hDLG possesses multiple protein‐binding domains, including three PDZ domains, an SH3 domain, a HOOK domain and a guanylate kinase‐like (GK) domain.Results: We studied the significance of the PDZ, SH3, HOOK and GK domains in the cytoplasmic localization of hDLG. We found that mutation of the SH3 or GK domain, but not the PDZ domain, resulted in a re‐localization of hDLG to the nucleus. Furthermore, hDLG was found to possess a potential nuclear localization signal in the HOOK domain.Conclusion: These results suggest that the SH3, HOOK and GK domains of hDLG are important for its cytoplasmic localization.
Joint estimation of AVO and kinematic parameters
Authors: Grion S. , Mazzotti A. , Spagnolini U. 
Published: March 2003

Conventional amplitude‐versus‐offset (AVO) analysis such as linear fitting of isotime samples after NMO correction does not give reliable results in the presence of interfering reflections or velocity errors. For this reason we propose a new method that is able to remove interference effects on the AVO of the target reflection and minimize the effects of residual moveout. The method is based on the minimization of the difference between observed data and a model that includes theoretical descriptions of the AVO and traveltimes. This minimization is carried out jointly with respect to AVO and kinematic parameters (velocities and traveltimes) and requires the a priori knowledge of the propagating wavelet. The kinematic parameters are given by the NMO equation extended to the fourth‐order term and the AVO is described as a linear combination of a set of orthogonal functions. The AVO functions are derived from a statistical model of reflection amplitude in the presence of velocity error.Applications to synthetic and real data demonstrate the ability of the method to attenuate distortion effects on the AVO of the primary reflection by interfering coherent noise. The real data example pertains to a marine case where the primary event is contaminated by multiple reflections generated in the water layer and by another event, reflected from an interface deeper than the target, that merges with the examined reflections at the far‐offsets. This causes a subtle tuning that distorts the AVO of the target. Our method attenuates the effects of the multiples and discriminates the ‘double event’ nature of the target reflection at the far‐offsets.
An approximate analytical approach to compute geoelectric dipole–dipole responses due to a small buried cube
Authors: Szalai Sándor , Szarka László 
Published: March 2003

A simple analytical solution is presented for computing direct current (DC) electric field distortion due to a small cube in a homogeneous half‐space, measured with a dipole–dipole array on the surface. Both the transmitter and the receiver may have any orientation; furthermore their position on the horizontal surface and the depth of the cube can be freely selected. It is shown that a simple approximate analytical method may replace more complicated 3D numerical modelling algorithms.The approximation lies in the linearization of the problem: the secondary source (i.e. the cube) is considered as a system of three perpendicular electric dipoles. In spite of this first‐order approximation, in the case of realistic depths z (zR≈0.1–0.5, where R is the transmitter–receiver distance), this approximate solution fits very well with true 3D numerical modelling results, and with analogue modelling results if aR≤0.1, where a is the length of the side of the cube. Due to its simplicity, this method could be used for computing DC field distortion effects, estimating parameter‐sensitivities, or even determining some initial models for further inversions.
Compressional‐wave Q estimation from full‐waveform sonic data
Authors: Dasios A. , Astin T.R. , McCann C. 
Published: March 2003

There is significant evidence that the anelastic loss of seismic energy is linked to petrophysical properties such as porosity, permeability and clay content. Thus, reliable estimation of anelastic attenuation from seismic data can lead to improved methods for the prediction of petrophysical properties. This paper is concerned with methods for the estimation of attenuation at sonic frequencies (5–30 KHz) from in situ data. Two independent methods have been developed and tested for estimating compressional‐wave attenuation from full‐waveform sonic data. A well‐established technique, the logarithm spectral ratio (LSR) method, is compared with a new technique, the instantaneous frequency (IF) method. The LSR method uses the whole spectrum of the seismic pulse whilst the IF method uses a carefully estimated value of instantaneous frequency which is representative of the centre frequency of the pulse. In the former case, attenuation estimation is based on the relative variation of amplitudes at different frequencies, whilst in the latter case it is based on the shift of the centre frequency of the pulse to lower values during anelastic wave propagation. The IF method does not assume frequency independence of Q which is a necessary assumption for the LSR method, and it provides a stable frequency log, the peak instantaneous frequency (PIF) log, which may be used as an indicator for attenuation under certain limitations. The development and implementation of the two methods is aimed at minimizing the effect of secondary arrivals, such as leaky modes, and involved a series of parameter tests. Testing of the two methods using full‐waveform sonic data of variable quality, obtained from a gas‐bearing sandstone reservoir, showed that the IF method is in general more stable and suitable for full‐waveform sonic data compared with the LSR method. This was evident especially in data sets with high background noise levels and wave‐interference effects. For good quality data, the two methods gave results that showed good agreement, whilst comparison with other log types further increased confidence in the results obtained. A significant decrease (approximately 5 KHz) in the PIF values was observed in the transition from an evaporite/shale sequence to the gas‐bearing sandstone. Average Q values of 54 and 51 were obtained using good quality data from a test region within the gas‐saturated sandstone reservoir, using the LSR and IF methods, respectively.