bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying woodland structure and habitat quality for birds using airborne laser scanning
Authors: Hinsley S. A. , Hill R. A. , Gaveau D. L. A. , Bellamy P. E. 
Published: March 2003

Summary

Vegetation height across a 157‐ha deciduous woodland was estimated using an airborne remote‐sensing technique, airborne laser scanning (ALS), and the data obtained were used to produce a three‐dimensional map of the canopy surface of the entire wood.
Field‐based estimates of a tree canopy density index were compared with mean vegetation height calculated from the ALS data for sample areas of 54 × 54 m2 centred on each of 36 nestboxes within the wood. Canopy density index increased with mean vegetation height, such that height explained 86% of the variation in the density index. Thus remote‐sensed height could be used as a surrogate for the field‐based estimates.
Mean chick masses (mass being used as a measure of habitat quality) for Great Tits (Parus major L.) and Blue Tits (P. caeruleus L.) using the boxes were also examined in relation to the ALS mean vegetation height for the same sample areas.
For Blue Tits, mean chick mass at 11 days of age increased with vegetation height around the nestbox, but for Great Tits, the relationship was negative. Possible reasons for this difference are discussed, but the results should be treated with caution because sample sizes were small.
The application of ALS in woodland ecology is discussed.
Are associational refuges species‐specific?
Authors: Hambäck P. A. , Pettersson J. , Ericson L. 
Published: March 2003

Summary

Associational refuges – reduced herbivory on plants in presence of other plant species – may be caused by general and species‐specific plant characteristics. However, the species specificity of associational refuges has rarely been evaluated.
This study examined the species specificity of one known example of associational refuges, the forb Lythrum salicaria and the monophagous insect herbivores Galerucella calmariensis, G. pusilla and Nanophyes marmoratus. The underlying mechanism was examined in order to evaluate connections between mechanisms and species specificity.
Laboratory studies showed that N. marmoratus but not Galerucella individuals were attracted by odour from undamaged host plants, and that neither species was distracted by odour from Myrica gale.
Field experiments showed that three non‐host plant neighbours with an appearance similar to M. gale, and artificial shrubs, reduced the abundance and egg‐laying of Galerucella species by 70–90%. The abundance of N. marmoratus was increased 18‐fold on plants in thickets compared with outside.
. The different responses by N. marmoratus and the Galerucella species to plant neighbours appear to be because N. marmoratus, but not Galerucella, uses olfactory information in the initial host‐finding process.
Foraging effort in relation to the constraints of reproduction in free‐ranging albatrosses
Authors: Shaffer S. A. , Costa D. P. , Weimerskirch H. 
Published: March 2003

Summary

Theoretical models predict that animals will vary their effort to maximize different currencies such as time and energy when the constraints of reproduction change during breeding, but this has been poorly studied in free‐ranging animals.
Foraging effort (energy per unit time) was examined by comparing mass changes, foraging costs and activity‐specific behaviours of Wandering Albatrosses (Diomedea exulans Linnaeus) during the incubation and chick‐brooding stages. In 1998, 38 albatrosses (20 during incubation and 18 during brooding) were injected with doubly labelled water and equipped with satellite transmitters and activity data loggers.
During incubation, albatrosses travelled 3·7 times farther and were at sea 3·2 times longer, yet foraging costs were significantly lower than trips made during brooding (incubation 4·52 ± 0·50 SD W kg−1vs brooding 4·98 ± 0·55 SD W kg−1).
The rate of daily mass gain decreased significantly with time at sea during incubation whereas the rate of daily mass gain increased significantly with time at sea during brooding.
Foraging effort was higher during brooding, suggesting that birds were minimizing time at sea to maximize the rate of food delivery to chicks. In contrast, foraging effort was lower during incubation, suggesting that birds were maximizing time at sea and minimizing the energy costs of foraging.
Foraging costs were also different between sexes. However, this was related to body size differences and not to differences in foraging effort as suggested in previous studies.
Identification of receptors and Smad proteins involved in activin signalling in a human epidermal keratinocyte cell line
Authors: Shimizu Akira , Kato Mitsuyasu , Nakao Atsuhito , Imamura Takeshi , Ten Dijke Peter , Heldin Carl‐Henrik , Kawabata Masahiro , Shimada Shinji , Miyazono Kohei 
Published: March 2003

Background:Activin A is a multifunctional protein, which is a member of the transforming growth factor‐β (TGF‐β) superfamily. Smad proteins have recently been shown to transduce signals for the TGF‐β superfamily of proteins, and Smad2 was implicated in activin signalling in Xenopus embryos.Results:We identified the receptors and Smad proteins activated by activin A in a human epidermal keratinocyte cell line, HaCaT. The major activin receptors expressed on HaCaT cells were activin type II receptor (ActR‐II) and activin type IB receptor (ActR‐IB). We have also shown that in HaCaT cells, activin A induced the phosphorylation of Smad3 and, to a lesser extent, of Smad2. On the other hand, TGF‐β induced an efficient phosphorylation of both Smad2 and Smad3. Activin A preferentially induced the nuclear translocation of Smad3 in HaCaT cells, whereas TGF‐β strongly induced the nuclear translocation of Smad2, as well as other Smads. Moreover, a constitutively active form of ActR‐IB efficiently stimulated the formation of a heteromeric complex between Smad3 and Smad4 in COS cells transfected with Smad cDNAs.Conclusions:These results suggest that activin A binds to a receptor complex of ActR‐II and ActR‐IB, and preferentially activates Smad3 in HaCaT human keratinocytes.
Regulatory mechanisms in expression of the traY‐I operon of sex factor plasmid R100: involvement of traJ and traY gene products
Authors: Taki Keiko , Abo Tatsuhiko , Ohtsubo Eiichi 
Published: March 2003

Background:The plasmid R100 encodes tra genes essential for conjugal DNA transfer in Escherichia coli. Genetic evidence suggests that the traJ gene encodes a positive regulator for the traY‐I operon, which includes almost all the tra genes located downstream of traJ. The molecular mechanism of regulation by TraJ, however, is not yet understood. traY is the most proximal gene in the traY‐I operon. TraY promotes DNA transfer by binding to a site, sbyA, near the origin of transfer. TraY is suggested to have another role in regulation of the traY‐I operon, since it binds to two other sites, named sbyB and sbyC, located in the region preceding traY‐I.Results:Using a traY‐lacZ fusion gene, we showed that the traY‐I operon was expressed only in the presence of traJ. The TraJ‐dependent expression of traY‐I required the E. coliarcA gene, which encodes a host factor required for conjugation. TraJ‐dependent transcription occurred from a promoter (named pY) located upstream of traY‐I. The isolated TraJ protein was found to bind to a dyad symmetry sequence, named sbj (specific binding site of TraJ), which existed in the intergenic region between traJ and traY‐I. We also demonstrated that TraY repressed the TraJ‐dependent expression of traY‐I at the TraY binding sites, sbyB and sbyC, which overlapped with pY.Conclusions:TraJ is a protein which binds to the sbj site in the region upstream of the promoter pY and positively regulates expression of the traY‐I operon in the presence of the E. coliarcA gene. Since sbj is located 93 bp upstream of pY in the intergenic region between traJ and traY‐I, TraJ presumably contacts with a transcription apparatus to promote transcription from pY. TraY, which is known to activate the initiation of conjugal DNA transfer, has a new role in the transcriptional autoregulation of traY‐I expression. At levels which are sufficient to initiate conjugal DNA transfer, TraY represses traY‐I transcription in the presence of TraJ.
AMY‐1, a novel C‐MYC binding protein that stimulates transcription activity of C‐MYC
Authors: Taira Takahiro , Maëda Junko , Onishi Takako , Kitaura Hirotake , Yoshida Shu , Kato Hiroyuki , Ikeda Masako , Tamai Katsuyuki , M. Iguchi‐Ariga Sanae M. , Ariga Hiroyoshi 
Published: March 2003

BackgroundThe c‐myc proto‐oncogene has been suggested to play key roles in cell proliferation, differentiation, transformation and apoptosis. A variety of functions of C‐MYC, the product of c‐myc, are attributed to protein–protein interactions with various cellular factors including Max, YY1, p107, Bin1 and TBP. Max and YY1 bind to the C‐terminal region of C‐MYC, while p107, Bin1 and TBP bind to the N‐terminal region covering myc boxes. The N‐terminal region is involved in all the biological functions of C‐MYC, and different proteins are therefore thought to interact with the N‐terminal region of C‐MYC to display different functions.ResultsWe cloned two cDNAs which encode a novel C‐MYC‐binding protein of 11 kDa, designated AMY‐1 (Associate of C‐MYC). The two cDNAs, AMY‐1L and AMY‐1S, derived from alternative usage of polyadenylation signals, code for the same protein of 11 kDa. AMY‐1 was bound via its C‐terminal region to the N‐terminal region of C‐MYC (amino acids nos 58–148) corresponding to the transactivation domain. AMY‐1 was localized in the cytoplasm in cells expressing c‐myc at low levels, but in the nucleus in the cells of a high c‐myc expression in transiently transfected cells. A similar difference in endogenous AMY‐1 localization was observed during the cell cycle: AMY‐1 translocated from cytoplasm to nucleus during the S phase when c‐myc expression was increased. AMY‐1 by itself did not recognize the E‐box element, the MYC/Max binding sequence, nor did it transactivate via the element, but stimulated the activation of E‐box‐regulated transcription by MYC/Max. FISH analyses revealed that the amy‐1 gene was located at 1p32.2–1p33 in human genome.ConclusionsAMY‐1 is a 11 kDa protein which binds to the N‐terminal region of C‐MYC and stimulates the activation of E‐box‐dependent transcription by C‐MYC. AMY‐1, which mostly localizes in the cytoplasm, translocates into the nucleus in the S phase of the cell cycle upon an increase of c‐myc expression, and may thus control the transcriptional activity of C‐MYC.
Disruption of the midkine gene (Mdk) resulted in altered expression of a calcium binding protein in the hippocampus of infant mice and their abnormal behaviour
Authors: Nakamura Eishin , Kadomatsu Kenji , Yuasa Shigeki , Muramatsu Hisako , Mamiya Takayoshi , Nabeshima Toshitaka , Fan Qi‐Wen , Ishiguro Kazuhiro , Igakura Tadahiko , Matsubara Shuichiro , Kaname Tadashi , Horiba Mitsuru , Saito Hidehiko , Muramatsu Takashi 
Published: March 2003

Background:Midkine (MK) is a growth factor implicated in the development and repair of various tissues, especially neural tissues. However, its in vivo function has not been clarified.Results:Knockout mice lacking the MK gene (Mdk) showed no gross abnormalities. We closely analysed postnatal brain development in Mdk(–/–) mice using calcium binding proteins as markers to distinguish neuronal subpopulations. Intense and prolonged calretinin expression was found in the dentate gyrus granule cell layer of the hippocampus of infant Mdk(–/–) mice. In infant Mdk(+/+) mice, calretinin expression in the granule cell layer was weaker, and had disappeared by 4 weeks after birth, when calretinin expression still persisted in Mdk(–/–) mice. Furthermore, 4 weeks after birth, Mdk(–/–) mice showed a deficit in their working memory, as revealed by a Y‐maze test, and had an increased anxiety, as demonstrated by the elevated plus‐maze test.Conclusion:Midkine plays an important role in the regulation of postnatal development of the hippocampus.
Expression of the Vax family homeobox genes suggests multiple roles in eye development
Authors: Ohsaki Kanae , Morimitsu Toshiharu , Ishida Yoko , Kominami Ryo , Takahashi Naoki 
Published: March 2003

BackgroundHomeobox gene products are thought to regulate target genes involved in the regional specification of tissues and organs. Several genes play roles in eye development.ResultsWe isolated two new mouse homeobox genes, Vax1 and Vax2, expressed in retina primordium. The two genes share the same gene organization, consisting of three exons with predicted amino acid sequences identical in the homeodomain but diversified in other regions. At 9.5 days post coitum, both Vax genes were expressed in optic vesicles. At 11.5–14.5 dpc, Vax1 became restricted to the optic stalk, while Vax2 was expressed in the ventral half of the neural retina. Mapping of Vax2 between D6Mit3 and D6Mit8 on chromosome 6 indicated a possible linkage with Emx1.ConclusionsThe expression patterns of Vax genes suggest separate and specific involvement in eye development. Vax1 may contribute to differentiation of the neuroretina, pigmented epithelium and optic stalk, while Vax2 could function in the establishment of the dorso‐ventral axis of the retina and the visual system. The chromosomal location of Vax2 suggests that Vax2‐Emx1 and Vax1‐Emx2 arose by chromosome duplication of the same ancestral gene.
Fission yeast APC/cyclosome subunits, Cut20/Apc4 and Cut23/Apc8, in regulating metaphase‐anaphase progression and cellular stress responses
Authors: Yamashita Yukiko M. , Nakaseko Yukinobu , Kumada Kazuki , Nakagawa Takashi , Yanagida Mitsuhiro 
Published: March 2003

BackgroundThe 20S cyclosome/APC complex promotes metaphase–anaphase transition by ubiquitinating its specific substrates such as mitotic cyclins and anaphase inhibitor Cut2/Pds1/securin. The complex has been shown to contain more than 10 proteins in budding yeast and frog. In fission yeast, however, only five (Cut4, Cut9, Nuc2, Apc10, Hcn1) have been identified.ResultsMore than five hundred temperature‐sensitive mutants were screened for identifying those defective in mitotic anaphase. Fifty‐five showed the cut (cell untimely torn) phenotype or metaphase‐arrest phenotypes, 27 of them locating at new loci. Their extracts were run in sucrose gradient centrifugation, and four showed alterations in the sedimentation profiles. The gene products of cut20+ and cut23+ were thus identified. Phenotypes of cut20–100 mutant highly resemble cut4–533 in many ways: they are hypersensitive to canavanine and CdCl2, and suppressed by PKA‐inactivating regulators, cAMP‐dependent phosphodiesterase and PKA regulatory subunits. Cut20 interacts closely with Cut4 in the assembly process of cyclosome. But cut20 mutant differs from cut4, as a novel gene stw1+ suppresses cut20 mutant but not cut4. cut23–194 mutant cells are sterile and blocked at metaphase, but does not show sensitivity to the stress and cAMP. TPR repeat‐containing Cut23 may not be the stable component of APC/cyclosome, and its level significantly fluctuates during cell cycle. Cut23 may be ubiquitinated and degraded in a cell cycle dependent fashion.ConclusionsWe identified two new subunits of fission yeast cyclosome/APC complex. Our observations indicate that cyclosome components are divided into several subgroups with distinctly different roles.
Tuning of the porin expression under anaerobic growth conditions by His‐to‐Asp cross‐phosphorelay through both the EnvZ‐osmosensor and ArcB‐anaerosensor in Escherichia coli
Authors: Matsubara Masahiro , Kitaoka Shin‐ichi , Takeda Shin‐ichiro , Mizuno Takeshi 
Published: March 2003

BackgroundWidespread bacterial signal transduction circuits are generally referred to as ‘two‐component systems’ or ‘histidine (His)‐to‐aspartate (Asp) phosphorelays.’ In Escherichia coli, as many as 30 distinct His‐to‐Asp phosphorelay signalling pathways operate in response to a wide variety of environmental stimuli, such as medium osmolarity and anaerobiosis. In this regard, it is of interest whether or not some of them together constitute a network of signalling pathways through a physiologically relevant mechanism (often referred to as ‘cross‐regulation’). We have addressed this issue, with special reference to the osmo‐responsive EnvZ and anaero‐responsive ArcB phosphorelay signalling pathways in E. coli.ResultsUnder standard aerobic growth conditions, it is well known that the osmoregulatory profile of the outer membrane porins (OmpC and OmpF) is mainly regulated by the EnvZ‐OmpR phosphorelay system in response to medium osmolarity. In this study, it was found that, under anaerobic growth conditions, E. coli cells exhibit a markedly altered expression profile of OmpC and OmpF This profile was significantly different from that observed for the cells grown aerobically. Results from extensive genetic studies showed that, under such anaerobic growth conditions, the arcB gene encoding the anaero‐sensory His‐kinase appears to be an auxiliary genetic determinant that regulates the expression profile of porins. We then provided several lines of in vivo and in vitro evidence, which taken together, supported the following conclusions.ConclusionsUnder anaerobic growth conditions, porin expression is tuned not only by the authentic osmo‐resposive EnvZ sensor, but also by the anaero‐responsive ArcB sensor, in an OmpR‐dependent manner. It is suggested that such ArcB‐mediated cross‐regulation plays a physiological role by integrating anaerobic respiratory signals into the porin regulation in E. coli anaerobiosis. The proposed model is a clear example of the interplay of two distinct His‐to‐Asp phosphorelay signalling pathways.
Expression and characterization of nonmammalian selenoprotein P in the zebrafish,Danio rerio
Authors: Tujebajeva Rosa M. , Ransom David G. , Harney John W. , Berry Marla J. 
Published: March 2003

Selenoprotein P is a protein of considerable intrigue, due to its unusual composition and requirements for its biosynthesis. Whereas most selenoproteins contain a single selenocysteine residue, the human, bovine and rodent selenoprotein P genes encode proteins containing 10–12 selenocysteines. Selenoprotein P genes have, to date, only been reported in mammals, and the function of the protein remains elusive.Herein, we report the identification and characterization of nonmammalian selenoprotein P in the zebrafishDanio rerio. Sequencing of the cDNA revealed the presence of 17 selenocysteine codons, the highest number reported in any protein. Two histidine‐rich regions present in the mammalian selenoprotein P sequences are conserved in the zebrafish protein, and two SECIS elements are present in the 3′ untranslated region. Whole‐mountin situhybridization of zebrafish embryos revealed high levels of expression of selenoprotein P mRNA in fertilized eggs and in the yolk sac of developing embryos. Transient transfection of the cDNA in mammalian cells resulted in efficient expression of the full‐length secreted selenoprotein. A single N‐glycosylation site is predicted, and shown to be utilized.Discovery of selenoprotein P in the zebrafish opens a previously unavailable avenue for genetic investigation of the functions of this unusual protein.
Ankycorbin: a novel actin cytoskeleton‐associated protein
Authors: Peng Ying‐Feng , Mandai Kenji , Sakisaka Toshiaki , Okabe Noriko , Yamamoto Yasunori , Yokoyama Shigekazu , Mizoguchi Akira , Shiozaki Hitoshi , Monden Morito , Takai Yoshimi 
Published: March 2003

Actin cytoskeleton structures are essential for a wide variety of cell functions, including cell shape change, cell motility, cell adhesion, cell polarity and cytokinesis. Many actin filament (F‐actin)‐binding proteins have been isolated and implicated in the maintenance and reorganization of actin cytoskeleton structures.We purified here a novel protein with a molecular mass of about 125 kDa (p125) from rat liver. We cloned its cDNA from a mouse kidney cDNA library and determined its nucleotide and deduced amino acid sequences. p125 was a protein of 979 amino acids with a calculated Mr of 108 847. p125 contained six ankyrin repeats in the N‐terminal region and a domain predicted to form a coiled‐coil structure in the C‐terminal region. We named p125 ankycorbin (ankyrin repeat‐ and coiled‐coil structure‐containing protein). Northern blot analysis indicated that ankycorbin was ubiquitously expressed in all the tissues examined. Immunofluorescence and immunoelectron microscope analyses revealed that ankycorbin was associated with the cortical actin cytoskeleton structures in terminal web and cell‐cell adhesion sites and stress fibres. However, ankycorbin did not directly bind to F‐actin as estimated by the F‐actin co‐sedimentation assay.These results indicate that ankycorbin is indirectly associated with the actin cytoskeleton structures, presumably through an unidentified factor and suggest that it is involved in their maintenance and/or reorganization.
Two proteins, YfiA and YhbH, associated with resting ribosomes in stationary phase Escherichia coli
Authors: Maki Yasushi , Yoshida Hideji , Wada Akira 
Published: March 2003

Ribosomes in Escherichia coli change their composition and conformation in the stationary phase. Ribosome modulation factor (RMF) and ribosomal protein S22 are known to be associated with stationary phase ribosomes. RMF association causes the loss of translational activity and the dimerization of 70S ribosomes into 100S ribosomes, which may increase cell survival in the stationary phase.Two weakly acidic proteins having related amino acid sequences were found to be associated with E. coli ribosomes in the stationary phase. These proteins are the products of ORFs named yfiA and yhbH. The sum of the copy numbers of their product proteins, YfiA and YhbH, in the ribosomal particles was low in the log phase, but increased to nearly one in the stationary phase. YfiA was found in the 70S ribosomal fraction rather than the 100S. On the other hand, YhbH was detected exclusively in the 100S ribosomal fraction. When the stationary phase cells were transferred to fresh medium, YfiA and YhbH were found in the 70S ribosomal fraction, but not in the polysome fraction.Two proteins, YfiA and YhbH, associated with E. coli ribosomes were found to accumulate in the stationary phase, leading to the formation of several types of ribosomes. They are not likely to have roles in the elongation step of the translation in log phase cells, but are likely to be involved in the stabilization and preservation of ribosomes in the stationary phase, which might be necessary for cell survival.