bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leaf‐level nitrogen‐use efficiency of canopy and understorey species in a beech forest
Authors: Yasumura Y. , Hikosaka K. , Matsui K. , Hirose T. 
Published: March 2003

Summary

In a forest stand, canopy and understorey species grow at completely different irradiances and consequently with different carbon and nitrogen availability ratios. We studied how the difference in growth irradiance influenced plant N use in a mature beech forest.
We defined leaf‐level nitrogen‐use efficiency (NUEL) as the amount of the leaf dry mass produced per unit N taken up by leaves. NUEL was similar between the canopy species (Fagus crenata) and the understorey species (Lindera umbellata and Magnolia salicifolia).
NUEL was analysed further as the product of two components: leaf‐level N productivity (NPL) and mean residence time of leaf N (MRTL). The canopy species had significantly larger NPL and significantly shorter MRTL than the understorey species.
As the photosynthetic capacity was similar among the species, different NPL between the species was attributable largely to the difference in light conditions to which their leaves were exposed.
The difference in MRTL was not attributable to potential efficiency of N resorption (REFF) determined at leaf senescence, but to actual REFF, which depended on the amount of green leaf lost before full senescence. The canopy species had significantly smaller actual REFF because of strong wind actions in the canopy.
Although the canopy species realized higher NPL by virtue of high irradiance, it had shorter MRTL due to wind damage to pre‐senescent leaves. On the other hand, the canopy species had shorter NPL under shady conditions, but had longer MRTL with little wind damage. Interplay of local environmental factors such as light and wind strongly influenced N use by plants in the beech forest.
Molecular cloning of cDNA and tissue‐specific expression of the gene for SII‐K1, a novel transcription elongation factor SII
Authors: Taira Yuichiro , Kubo Takeo , Natori Shunji 
Published: March 2003

BackgroundTranscription elongation factor SII has been shown to promote read‐through by RNA polymerase II of pausing sites within various eukaryotic genes in vitro by inducing cleavage of the 3′‐end of the nascent transcript in the ternary elongation complex. Recently, we showed that various mouse tissues contain multiple SII‐related proteins. Of these, ‘general SII’ was ubiquitously expressed, whereas the others were expressed in a tissue‐specific manner. We have identified testis‐specific SII (SII‐T1) and shown that it was expressed exclusively in spermatocytes.ResultsA new SII cDNA clone (pSII‐K1) was isolated from mouse kidney. This clone contained an open reading frame which encoded a protein consisting of 347 amino acid residues (SII‐K1). A comparison of the amino acid sequences of SII‐K1 with those of general SII and SII‐T1 revealed that their amino‐ and carboxy‐terminal regions were very similar, but that the sequence of the 95 internal residues (87/181) was unique to each. The recombinant SII‐K1 produced in Escherichia coli stimulated RNA polymerase II as did general S‐II. The gene for SII‐K1 was found to be expressed strongly in the heart, liver, skeletal muscle and kidney, but not in other tissues examined. Contrary to the expression of the general SII gene, the SII‐K1 gene was expressed only in 15‐ and 17‐day‐old embryos during mouse embryonic development.ConclusionsWe identified a novel member of SII family transcription elongation factor named SII‐K1. This factor was expressed exclusively in the heart, liver, kidney and skeletal muscle. During mouse embryonic development, no significant expression of the SII‐K1 gene was detected before the formation of these tissues.
Developmental patterning in chondrocytic cultures by morphogenic gradients: BMP induces expression of Indian hedgehog and Noggin
Authors: Kameda Takashi , Koike Chika , Saitoh Kanako , Kuroiwa Atsushi , Iba Hideo 
Published: March 2003

BackgroundThe maturation of chondrocytes is essential for endochondral bone formation. The Indian Hedgehog (Ihh) gene is expressed in prehypertropic chondrocytes and has been proposed to regulate chondrocyte maturation. While such secretary factors as PTHrP and BMP are thought to be involved in Ihh expression, the mechanism of the restricted expression of Ihh is not clear.ResultsUsing primary chondrocytes, we have developed here a modified micromass culture (MM‐C) system that allows the formation of concentration gradients of secreted factors, expressed either endogenously or retrovirally, from each of plural micromass cultures on a single plate. Using this system, we determined that chondrocytes create the inhibitory micro‐environment, partly dependent on PTHrP secretion, for the Ihh expression. We also showed that retrovirally induced BMP‐2 induces the expression of both Ihh and Noggin (encoding the BMP‐inactivating protein), and we further present evidence that a negative‐feedback loop involving Noggin might account for the precise localization of BMP signalling for Ihh induction.ConclusionThese results suggest that the expression of the Ihh gene in cartilage is regulated by several mechanisms that include the secretion of inhibitory factors (including PTHrP) and the negative‐feed back loop formed by BMPs and Noggin.
Identification of engrailed promoter elements essential for interactions with a stripe enhancer in Drosophila embryos
Authors: Orihara Minako , Hosono Chie , Kojima Tetsuya , Saigo Kaoru 
Published: March 2003

BackgroundThe structures and functions of promoter sequences of most genes have been analysed using in vitro transcription and/or cultured cell systems, neither possessing tissue‐specific enhancers. Promoter–enhancer interactions in vivo, in particular, during ontogeny, are still poorly understood.ResultsWe have established a new method for the assessment of promoter activity in cells that participate in fly body formation, using the UAS/GAL4 system. A functional analysis was then conducted on the promoter sequence of the engrailed gene in Drosophila embryos. A 38‐bp‐long sequence, terminating with an initiator or RNA start site and a downstream promoter element, was found to be capable of receiving activation signals from the engrailed stripe enhancer. Transcriptional efficiency was improved significantly by the presence of upstream promoting elements, most functionally replaceable with synthetic GAGA factor binding sites.ConclusionsWe identified the in vivo minimum promoter of engrailed and demonstrated that the GAGA factor binding sites serve primarily as quantitative elements which augment transcriptional efficiency. Evidence was also obtained that indicated that not only enhancer but also promoter sequences were involved in the determination of the tissue‐specificity of gene expression.
Negative regulation of theptsoperon by Mlc: mechanism underlying glucose induction inEscherichia coli
Authors: Tanaka Yuya , Kimata Keiko , Inada Toshifumi , Tagami Hideaki , Aiba Hiroji 
Published: March 2003

BackgroundTheptsoperon ofEscherichia coliconsists of three genesptsH,ptsIandcrr, each encoding for central components of the phosphoenolpyruvate: carbohydrate phosphotransferase system, HPr, enzyme I and IIAGlc, respectively. Transcription of theptsoperon is stimulated when glucose is present in the culture medium. One of the two major promoters, P0, is responsible for this glucose induction. However, no regulatory protein responsible for the glucose induction of theptsoperon has been identified yet and molecular mechanism by which glucose stimulates theptstranscription is not known.ResultsWe found by Northern blotting that theptsmRNA levels in cells lacking Mlc, a new global repressor of carbohydrate metabolism, were increased without external glucose and that the addition of glucose had no effect on theptsmRNA levels in the mutant cells. Western blotting revealed that the enzyme I level in themlc−cells was also elevated without glucose and no further increase in the enzyme I level was observed in the presence of glucose. S1 analysis revealed that transcription of the glucose‐sensitive promoter, P0, occurs constitutively in themlc−cells independently from the external glucose.In vitrotranscription studies indicated that Mlc strongly inhibited P0 transcription. DNase I footprinting experiment revealed that Mlc bound to P0 promoter region to prevent RNA polymerase binding at P0.ConclusionWe conclude that Mlc is a repressor for theptstranscription acting as a major regulatory protein involved in the glucose induction ofptsoperon. We propose that glucose induces theptstranscription by modulating the Mlc activity. The mechanism by which glucose modulates the Mlc action remains to be studied.
Similar and differential behaviour between the nectin‐afadin‐ponsin and cadherin‐catenin systems during the formation and disruption of the polarized junctional alignment in epithelial cells
Authors: Asakura Takeshi , Nakanishi Hiroyuki , Sakisaka Toshiaki , Takahashi Kenichi , Mandai Kenji , Nishimura Miyuki , Sasaki Takuya , Takai Yoshimi 
Published: March 2003

BackgroundWe have recently identified a novel cell‐cell adhesion system, named NAP system, which is localized at cadherin‐based cell‐cell adherens junctions (AJs). The NAP system is composed of at least nectin, afadin and ponsin. Nectin is an immunoglobulin‐like cell adhesion molecule. Afadin is an actin filament‐binding protein which associates nectin with the actin cytoskeleton. Ponsin is an afadin‐binding protein which furthermore binds to vinculin and provides a possible linkage of nectin‐afadin to cadherin‐catenin through vinculin. We compared here the behaviour of the NAP and cadherin‐catenin systems during the formation and disruption of the polarized junctional alignment in epithelial cells.ResultsAt the early stage of the formation of the polarized junctional alignment in MTD‐1 A cells, primordial spot‐like junctions were formed at the tips of thin cellular protrusions radiating from adjacent cells. Nectin, afadin, ponsin, cadherin and catenin were simultaneously recruited to these junctions. As the cell polarization proceeded, the spot‐like junctions were gradually fused to form belt‐like AJs where all these proteins were concentrated. The disruption of cell‐cell AJs in MDCK cells by culturing at a low Ca2+ concentration caused rapid endocytosis of cadherin, but not that of nectin or afadin. Addition of 12‐O‐tetradecanoylphorbol‐13‐acetate to the cells formed a tight junction‐like structure where nectin and afadin, but not cadherin, accumulated.ConclusionThese results indicate that the NAP and cadherin‐catenin systems show similar and differential behaviour during the formation and disruption of the polarized junctional alignment in epithelial cells.
Long range interaction of cis‐DNA elements mediated by architectural transcription factor Bach1
Authors: Yoshida Chikashi , Tokumasu Fuyuki , Hohmura Ken I. , Bungert Jörg , Hayashi Norio , Nagasawa Toshiro , Engel James Douglas , Yamamoto Masayuki , Takeyasu Kunio , Igarashi Kazuhiko 
Published: March 2003

BackgroundA central question in vertebrate transcriptional regulation is how cis‐regulatory modules, including enhancers, silencers and promoters, communicate with each other over long distances to mandate proper gene expression. In order to address this question we analysed protein/DNA interactions in the human β‐globin locus control region (LCR). One of the many proteins that are potentially implicated in LCR function is Bach1. Bach1 possesses a basic leucine zipper (bZip) domain, as well as a BTB/POZ domain that has been shown to be involved in the regulation of chromatin structure. Bach1 forms heterodimers with small Maf proteins through its leucine zipper and binds to
Maf
recognition
elements (MARE).ResultsUsing atomic force microscopy we visualized large looped DNA structures between MAREs located in different regulatory elements within the human β‐globin LCR that were mediated by Bach1/MafK heterodimers. The formation of these DNA loops required the Bach1 BTB/POZ protein interaction domain. Furthermore, in transfection studies we found that Bach1 repressed the enhancer activity of the LCR in a BTB/POZ domain‐dependent manner.ConclusionOur results suggest that Bach1 and other BTB/POZ transcription factors may represent a class of nuclear architectural proteins that mediate long range interactions between cis‐regulatory elements in order to regulate gene expression.
Region between α‐helices 3 and 4 of the Mad homology 2 domain of Smad4: functional roles in oligomer formation and transcriptional activation
Authors: Tada Keiichiro , Inoue Hirofumi , Ebisawa Takanori , Makuuchi Masatoshi , Kawabata Masahiro , Imamura Takeshi , Miyazono Kohei 
Published: March 2003

BackgroundSmad4 has a unique region of 35 amino acids between α‐helices 3 and 4 (termed H3/4 loop) of the Mad homology (MH) 2 domain. In order to elucidate the functional importance of the H3/4 loop, we prepared chimeric constructs of Smad4 containing the region corresponding to the α‐helix 3, H3/4 loop and α‐helix 4 of different Smads, including a chimera containing that of Smad2 (Smad4‐HL2).ResultsSmad4‐HL2 constitutively induced the transcriptional activation of p3TP‐Lux, a TGF‐β‐responsive reporter construct. However, co‐transfection of Smad2 with Smad4‐HL2 did not induce a further increase in the activation of p3TP‐Lux. Smad4‐HL2 did not induce the activation of pAR3‐Lux, which contains FAST1‐binding sites and is activated by a complex composed of FAST1, Smad2 and Smad4. Smad4‐HL2 formed a homo‐oligomer more efficiently than wild‐type Smad4 in mammalian cells. Moreover, Smad4‐HL2 bound to DNA containing the Smad‐binding sites with a gretaer affinity than the wild‐type Smad4.ConclusionSmad4‐HL2 spontaneously forms a homo‐oligomer, which may bind to DNA with relatively high affinity and induce transcriptional activation of p3TP‐Lux. The H3/4 loop of Smad4 may thus play a role in precluding the spontaneous oligomer formation of Smad4.
Mechanism of catabolite repression in the bgl operon of Escherichia coli: involvement of the anti‐terminator BglG, CRP‐cAMP and EIIAGlc in mediating glucose effect downstream of transcription initiation
Authors: Gulati Abhilasha , Mahadevan Subramony 
Published: March 2003

BackgroundExpression of the bgl operon of Escherichia coli, involved in the regulated uptake and utilization of aromatic β‐glucosides, is extremely sensitive to the presence of glucose in the growth medium. We have analysed the mechanism by which glucose exerts its inhibitory effect on bgl expression.ResultsOur studies show that initiation of transcription from the bgl promoter is only marginally sensitive to glucose. Instead, glucose exerts a more significant inhibition on the elongation of transcription beyond the rho‐independent terminator present within the leader sequence. Transcriptional analyses using plasmids that carry mutations in bglG or within the terminator, suggest that the target for glucose‐mediated repression is the anti‐terminator protein, BglG. Introduction of multiple copies of bglG or the presence of mutations that inhibit its phosphorylation by Enzyme IIBgl (BglF), result in loss of glucose repression. Studies using crp, cya and crr strains show that both CRP‐cAMP and the Enzyme IIAGlc (EIIAGlc) are involved in the regulation. Although transcription initiation is normal in a crp, cya double mutant, no detectable transcription is seen downstream of the terminator, which is restored by a mutation within the terminator. Transcription past the terminator is also partly restored by the addition of exogenous cAMP to glucose‐grown cultures of a crp+ strain. Glucose repression is lost in the crr mutant strain.ConclusionsThe results summarized above indicate that glucose repression in the bgl operon is mediated at the level of transcription anti‐termination, and glucose affects the activity of BglG by altering its phosphorylation by BglF. The CRP‐cAMP complex is also involved in this regulation. The results using the crr mutant suggest a negative role for EIIAGlc in the catabolite repression of the bgl genes.
Schnurri interacts with Mad in a Dpp‐dependent manner
Authors: Udagawa Yoshiyuki , Hanai Jun‐ichi , Tada Kei‐ichiro , Grieder Nicole C. , Momoeda Mikio , Taketani Yuji , Affolter Markus , Kawabata Masahiro , Miyazono Kohei 
Published: March 2003

BackgroundDecapentaplegic (Dpp) is a member of the transforming growth factor‐β superfamily. Dpp governs various developmental processes in Drosophila through the transcriptional regulation of a variety of genes. Signals of Dpp are transmitted from the cell membrane to the nucleus by Medea and Mad, both belonging to the Smad protein family. Mad was shown to bind to the Dpp‐responsive element in genes such as vestigial, labial, and Ultrabithorax. The DNA binding affinity of Smad proteins is relatively low, and requires other nuclear factor(s) to form stable DNA binding complexes. schnurri (shn) was identified as a candidate gene acting downstream of Dpp receptors, but its relevance to Mad has remained unknown.ResultsWe characterized the biochemical functions of Shn. Shn forms homo‐oligomers. Shn is localized in the nucleus, and is likely to have multiple nuclear localizing signals. Finally, we found that Shn interacts with Mad in a Dpp‐dependent manner.ConclusionsThe present results argue that Shn may act as a nuclear component of the Dpp signalling pathway through direct interaction with Mad.
Molecular beacon aptamer fluoresces in the presence of Tat protein of HIV‐1
Authors: Yamamoto Rika , Kumar Penmetcha K. R. 
Published: March 2003

BackgroundWe reported an aptamer, RNATat that binds to the Tat protein of HIV with two orders of magnitude greater (133‐fold) affinity over the TAR RNA of HIV‐1 and specifically inhibits the Tat‐dependent trans‐activation of transcription, both in vitro and in vivo (demonstrated in the accompanying article, Yamamoto et al., this issue pp. 371–388). We now report the use of aptamer‐derived oligomers to analyze the Tat of HIV and the possible applications of such constructs in the field of biosensors.ResultsTo make new molecular beacon, we constructed two RNA oligomers that derived from RNATat. To one of the split RNA oligomers that forms a hairpin structure, the fluorophore and quencher were attached at the 5′‐ and 3′‐ends, respectively. Specifically in the presence of Tat or its peptides, but not in the presence of other RNA binding proteins, the two oligomers undergo a conformational change to form a duplex that leads to relieving of fluorophore from the quencher, and thus a significant enhancement of the fluorescence of fluorescein was observed.ConclusionA novel strategy for exploiting aptamers in the analysis of Tat (analyte) has been described. A similar strategy could be used to study other analytes such as proteins and small molecules. In addition, the molecular beacon aptamer requires half the length of target sequence (eight nucleotides) in comparison with molecular beacons. Thus, it is conceivable that we could insert an analyte‐binding site into molecular beacons to convert them to signalling beacons.
Interaction between neurone and microglia mediated by platelet‐activating factor
Authors: Aihara Makoto , Ishii Satoshi , Kume Kazuhiko , Shimizu Takao 
Published: March 2003

BackgroundPlatelet‐activating factor (PAF) is a potent phospholipid mediator that plays various roles in neuronal function and brain development. The production and release of PAF in the brain has also been reported under various pathological conditions. However, neither the cell types and mechanism responsible for the synthesis of PAF nor its target cells have been fully identified.ResultsUsing primary culture cells derived from rat brain and a very sensitive assay method for PAF, we found that PAF was synthesized in neurones following stimulation with glutamic acid. PAF synthesis required activation of NMDA receptors and subsequent elevation of intracellular calcium ions. Microglia, which express functional PAF receptors to a high level, showed a marked chemotactic response to PAF. This chemotaxis is a receptor‐mediated process, as microglia from PAF‐receptor‐deficient mice did not show such a response. The activation of a pertussis‐toxin‐sensitive G‐protein and mitogen‐activated protein kinase presumably plays a role in intracellular signalling leading to chemotaxis.ConclusionsConsidering the cytoprotective and cytotoxic roles of microglia, PAF functions as a key messenger in neurone–microglial interactions.
Multiple downstream signalling pathways from ROCK, a target molecule of Rho small G protein, in reorganization of the actin cytoskeleton in Madin–Darby canine kidney cells
Authors: Takaishi Kenji , Matozaki Takashi , Nakano Katsutoshi , Takai Yoshimi 
Published: March 2003

In Madin–Darby canine kidney cells, Rho small G protein regulates formation of stress fibres, focal adhesions, and peripheral bundles through reorganization of the actin cytoskeleton. There are two morphologically distinguishable types of Rho‐regulated stress fibres: parallel and stellate. Of these, effects of Rho small G protein, mDia1 regulates the formation of parallel stress fibres, whereas ROCK regulates the formation of stellate stress fibres, peripheral bundles and focal adhesions. Both mDia1 and ROCK are direct downstream targets of Rho small G protein.The ROCK‐induced formation of stellate stress fibres is regulated mainly through the myosin light chain kinase‐dependent phosphorylation of myosin light chain and the LIM‐kinase‐dependent phosphorylation of cofilin. The ROCK‐induced formation of focal adhesions is mainly regulated through a downstream pathway of ROCK other than myosin light chain and cofilin. The ROCK‐induced formation of peripheral bundles is regulated at least through ERM proteins, but not through the myosin light chain or cofilin.Our present and previous findings suggest the presence of multiple downstream signalling pathways from ROCK to reorganization of the actin cytoskeleton in Madin–Darby canine kidney cells.
Mouse Peg9/Dlk1 and human PEG9/DLK1 are paternally expressed imprinted genes closely located to the maternally expressed imprinted genes: mouse Meg3/Gtl2 and human MEG3
Authors: Kobayashi Shin , Wagatsuma Hirotaka , Ono Ryuichi , Ichikawa Hitoshi , Yamazaki Masaaki , Tashiro Hiroyuki , Aisaka Kohzo , Miyoshi Naoki , Kohda Takashi , Ogura Atsuo , Ohki Misao , Kaneko‐Ishino Tomoko , Ishino Fumitoshi 
Published: March 2003

Genomic imprinting significantly influences development, growth and behaviour in mammals. Systematic screening of imprinted genes has been extensively carried out to identify the genes responsible for imprinted phenotypes and to elucidate the biological significance of this phenomenon. In this study, we applied DNA chip technology for isolating paternally expressed imprinted genes (Pegs). We compared the resulting expression profiles of parthenogenetic and fertilized control embryos to identify novel imprinted genes.A novel paternally expressed mouse imprinted gene, Peg9/Dlk1, was identified. Consistent with this finding, the paternal expression of its human homologue, PEG9/DLK1, was also confirmed. These two genes form imprinted gene clusters with the reciprocally imprinted mouse Meg3/Gtl2 and human MEG3 genes that we first identified on distal chromosome 12 and chromosome 14q32, respectively.As DNA chip technology allows us to quickly screen a large number of genes, using this technology to search for imprinted genes could accelerate the identification of genes responsible for human and mouse genetic diseases. Dlk1 and DLK1, which encode transmembrane proteins, have six EGF‐like repeats and show homology to the Delta gene in Drosophila melanogaster. Because of its homology to mammalian Delta homologues, PEG9/DLK1 may contribute to the scoliosis phenotype observed in maternal uniparental disomy 14 (mUPD14) patients.