bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting changes in community composition and ecosystem functioning from plant traits: revisiting the Holy Grail
Authors: Lavorel S. , Garnier E. 
Published: March 2003

Summary

The concept of plant functional type proposes that species can be grouped according to common responses to the environment and/or common effects on ecosystem processes. However, the knowledge of relationships between traits associated with the response of plants to environmental factors such as resources and disturbances (response traits), and traits that determine effects of plants on ecosystem functions (effect traits), such as biogeochemical cycling or propensity to disturbance, remains rudimentary.
We present a framework using concepts and results from community ecology, ecosystem ecology and evolutionary biology to provide this linkage. Ecosystem functioning is the end result of the operation of multiple environmental filters in a hierarchy of scales which, by selecting individuals with appropriate responses, result in assemblages with varying trait composition. Functional linkages and trade‐offs among traits, each of which relates to one or several processes, determine whether or not filtering by different factors gives a match, and whether ecosystem effects can be easily deduced from the knowledge of the filters.
To illustrate this framework we analyse a set of key environmental factors and ecosystem processes. While traits associated with response to nutrient gradients strongly overlapped with those determining net primary production, little direct overlap was found between response to fire and flammability.
We hypothesize that these patterns reflect general trends. Responses to resource availability would be determined by traits that are also involved in biogeochemical cycling, because both these responses and effects are driven by the trade‐off between acquisition and conservation. On the other hand, regeneration and demographic traits associated with response to disturbance, which are known to have little connection with adult traits involved in plant ecophysiology, would be of little relevance to ecosystem processes.
This framework is likely to be broadly applicable, although caution must be exercised to use trait linkages and trade‐offs appropriate to the scale, environmental conditions and evolutionary context. It may direct the selection of plant functional types for vegetation models at a range of scales, and help with the design of experimental studies of relationships between plant diversity and ecosystem properties.
Nutrient concentration, resorption and lifespan: leaf traits of Australian sclerophyll species
Authors: Wright I. J. , Westoby M. 
Published: March 2003

Summary

Most plants withdraw nutrients from leaves as they age, and redeploy them elsewhere in the plant. The proportion of nutrients resorbed and the residual nutrient concentration in senesced leaves are different but complementary indices of nutrient conservation via this process. A major spectrum of strategic variation runs from plant species with typically long leaf lifespan (LL), high leaf mass per area (LMA), low leaf nutrient concentrations, and low photosynthetic capacity, to species with the opposite characteristics. It is unknown to what extent either facet of resorption covaries with the LL–LMA spectrum.
Green‐leaf and senesced‐leaf N and P concentrations were quantified for 73 evergreen species from four sites in eastern Australia (nutrient‐rich and nutrient‐poor sites in each of two rainfall zones). Leaf nutrient concentrations in green and senesced leaves were negatively correlated with LL across all species and at most sites, especially if N2‐fixing species were excluded from analyses involving leaf N.
Proportional resorption did not differ with soil nutrients, as has been found elsewhere, nor was it correlated with LL. Green‐leaf and senesced‐leaf nutrient concentrations were lower for species on poorer soils. A simple model was described in which the proportion of resorbed vs soil‐derived nutrients deployed in new leaves is set by the relative cost of nutrients from the two sources. The model provides a prospective explanation for the observed differences between species from nutrient‐rich and nutrient‐poor habitats.
The results from this study provide support for the argument that selection to minimize nutrient losses has affected the residual nutrient concentration in senesced leaves, rather than proportional resorption per se. Further, variation among species in residual nutrient concentration was correlated with one of the key spectra of strategic variation between plant species, the leaf lifespan–LMA axis of variation.
BRAM1, a BMP receptor‐associated molecule involved in BMP signalling
Authors: Kurozumi Kimikazu , Nishita Michiru , Yamaguchi Kyoko , Fujita Takashi , Ueno Naoto , Shibuya Hiroshi 
Published: March 2003

BackgroundTGF‐β superfamily members elicit signals through the stimulation of serine/threonine‐kinase receptors. Recently, molecules associated with several TGF‐β family receptors have been cloned. One such molecule, the immunophilin FKBP12, has been reported to interact with TGF‐β family type I receptors. However, the identity of signalling specific molecules interacting with the receptor was unknown.ResultsTo clarify the factors mediating bone morphogenetic protein (BMP) receptor signalling, a cytoplasmic molecule associated with the BMP type IA receptor (BMPR‐IA) was isolated using the yeast two‐hybrid system. We designated the molecule BMP receptor associated molecule 1 (BRAM1). BRAM1 is an alternatively spliced form of BS69, a factor previously identified as an adenovirus E1A‐associated protein. BRAM1 was localized to the cytoplasmic region in mammalian cells, whereas BS69 is localized to the nucleus. BRAM1 bound specifically to BMPR‐IA in mammalian cells. The C‐terminal half of BRAM1 was found to be sufficient for binding to BMPR‐IA.ConclusionsBRAM1, a BMPR‐IA associated molecule, was isolated using the yeast two‐hybrid system, and found to associate specifically with BMPR‐IA. BRAM1 may thus serve as an interacting protein in the BMP signal pathway.
Involvement of CRM1, a nuclear export receptor, in mRNA export in mammalian cells and fission yeast
Authors: Watanabe Mina , Fukuda Makoto , Yoshida Minoru , Yanagida Mitsuhiro , Nishida Eisuke 
Published: March 2003

BackgroundCRM1, an evolutionarily conserved protein, was shown to be a receptor for leucine‐rich nuclear export signal (NES)‐dependent protein transport. In lower eukaryotes CRM1 is reported to be required for the export of mRNA, however, involvement of the NES‐dependent transport pathway in mRNA export in higher eukaryotes has not been established.ResultsWe have found that treatment of mammalian cells with leptomycin B (LMB), a specific inhibitor of CRM1, induces the nuclear accumulation of endogenous mRNA, probably due to the inhibition of its export. In fission yeasts, the nuclear accumulation of mRNA also occurred in cells treated with LMB or in a temperature‐sensitive crm1 mutant at a restrictive temperature. A synthetic mRNA that was injected into the nucleus of mammalian cultured cells was exported from the nucleus within 5 h. This export was inhibited by both wheat germ agglutinin and a temperature of 4 °C. Importantly, this mRNA export was inhibited by LMB or by an excess amount of the NES peptide‐conjugates. LMB treatment, on the other hand, rapidly induced the nuclear entry of RanBP1, a factor involved in the active nucleocytoplasmic transport, although the treatment did not interfere with a nuclear localization signal‐dependent transport system within 7 h.ConclusionThese results suggest that CRM1 is involved in mRNA export in eukaryotic cells.
Orientation specificity of the Lactococcus lactis Chi site
Authors: El Karoui Meriem , Schaeffer Matthieu , Biaudet Véronique , Bolotin Alexandre , Sorokin Alexeï , Gruss Alexandra 
Published: March 2003

BackgroundIn Escherichia coli, the Chi sequence modulates the activity of RecBCD, a powerful double‐stranded (ds) DNA exonuclease/helicase. Chi attenuates RecBCD exonuclease activity and stimulates homologous recombination in an orientation‐dependent manner. ChiEc is frequent and over‐represented on its genome, which is thought to be related to its role in dsDNA break repair. We previously identified a Chi‐like sequence (referred to as ChiLl) and an exonuclease/helicase in the Gram‐positive bacterium Lactococcus lactis. ChiLl and RexAB are functional analogues of ChiEc and RecBCD.ResultsWe report that ChiLl attenuates RexAB exonuclease activity and stimulates homologous recombination in an orientation‐dependent manner. Analysis of ChiLl distribution on the L. lactis chromosome reveals that ChiLl is frequent, highly over‐represented, and oriented with respect to the direction of replication.ConclusionOur results show that a single orientation of ChiLl interacts with RexAB. The active orientation is preferentially found on the replication leading strand of the L. lactis genome, consistent with a primary role of ChiLl in repair of dsDNA breaks at the replication fork. We propose that orientation‐dependence of Chi activity and over‐representation of Chi sequences on bacterial genomes may be conserved properties of exonuclease/helicase–Chi couples. Other properties of the Chi sequence distribution on the genomes might reflect more specific characteristics of each couple and of the host.
The paternal methylation imprint of the mouse H19 locus is acquired in the gonocyte stage during foetal testis development
Authors: Ueda Takayuki , Abe Kuniya , Miura Asuka , Yuzuriha Misako , Zubair Mohamad , Noguchi Motoko , Niwa Katsutoshi , Kawase Yosuke , Kono Tomohiro , Matsuda Yoichi , Fujimoto Hirokazu , Shibata Hideo , Hayashizaki Yoshihide , Sasaki Hiroyuki 
Published: March 2003

BackgroundGermline‐specific differential DNA methylation that persists through fertilization and embryonic development is thought to be the ‘imprint’ distinguishing the parental alleles of imprinted genes. If such methylation is to work as the imprinting mechanism, however, it has to be reprogrammed following each passage through the germline. Previous studies on maternally methylated genes have shown that their methylation imprints are first erased in primordial germ cells (PGCs) and then re‐established during oocyte growth.ResultsWe have examined the timing of the reprogramming of the paternal methylation imprint of the mouse H19 gene during germ cell development. In both male and female PGCs, the paternal allele is partially methylated whereas the maternal allele is unmethylated. This partial methylation is completely erased in the female germline by entry into meiosis, establishing the oocyte methylation pattern. In the male germline, both alleles become methylated, mainly during the gonocyte stage, establishing the sperm methylation pattern.ConclusionThe paternal methylation imprint of H19 is established in the male germline and erased in the female germline at specific developmental stages. The identification of the timings of the methylation and demethylation should help to identify and characterize the biochemical basis of the reprogramming of imprinting.
Ribonuclease H attack of leukaemic fused transcripts AML1‐MTG8(ETO) by DNA/RNA chimeric hammerhead ribozymes
Authors: Kozu Tomoko , Sugio Yasuhiro , Fukuyama Tomofusa , Sueoka Eisaburo , Otsuka Teruhisa , Akagi Kiwamu 
Published: March 2003

BackgroundCatalytic anti‐sense oligonucleotides might be useful tools for controlling specific gene expression. However, to obtain effective oligonucleotides of the desired function in vivo is still a difficult task.ResultsTo evaluate the usefulness of synthesized DNA/RNA hammerhead ribozymes targeting AML1‐MTG8 (ETO) leukaemic fusion transcripts in vivo, we analysed their effects on cell growth and the mechanism of action using isolated cell nuclei. These ribozymes inhibited the growth of leukaemic cell lines expressing the AML1 ‐MTG8 and degraded AML1‐MTG8 mRNA in isolated nuclei of these cells. However, the reactions gave rise to additional cleavage products. Systematic cleavage analyses using an anti‐sense oligonucleotide array revealed that the cleavage was induced by endogenous RNase H at specific sites, in accordance with their calculated melting temperature (Tm) values. With suppression of RNase H by sulfhydryl agents, the DNA/RNA ribozyme had a ribozyme catalytic activity. In addition, the ribozymes and anti‐sense oligonucleotides suppressed the AML1‐MTG8 protein in the leukaemic cells.ConclusionsThe DNA/RNA ribozymes inhibited cell growth primarily via anti‐sense effects, the main role of which was the activation of RNase H‐digestion by their DNA arms. In addition, the isolated nuclei provided a useful assay system for modelling in vivo conditions for the quantitative evaluation of anti‐sense/ribozyme activity.
The conserved nuclear receptor Ftz‐F1 is required for embryogenesis, moulting and reproduction in Caenorhabditis elegans
Authors: Asahina Masako , Ishihara Takeshi , Jindra Marek , Kohara Yuji , Katsura Isao , Hirose Susumu 
Published: March 2003

BackgroundNuclear receptors are essential players in the development of all metazoans. The nematode Caenorhabditis elegans possesses more than 200 putative nuclear receptor genes, several times more than the number known in any other organism. Very few of these transcription factors are conserved with components of the steroid response pathways in vertebrates and arthropods. Ftz‐F1, one of the evolutionarily oldest nuclear receptor types, is required for steroidogenesis and sexual differentiation in mice and for segmentation and metamorphosis in Drosophila.ResultsWe employed two complementary approaches, direct mutagenesis and RNA interference, to explore the role of nhr‐25, a C. elegans ortholog of Ftz‐F1. Deletion mutants show that nhr‐25 is essential for embryogenesis. RNA interference reveals additional requirements throughout the postembryonic life, namely in moulting and differentiation of the gonad and vulva. All these defects are consistent with the nhr‐25 expression pattern, determined by in situ hybridization and GFP reporter activity.ConclusionsOur data link the C. elegans Ftz‐F1 ortholog with a number of developmental processes. Significantly, its role in the periodical replacement of cuticle (moulting) appears to be evolutionarily shared with insects and thus supports the monophyletic origin of moulting.
In vitro analysis of STAT5 activation by granulocyte‐macrophage colony‐stimulating factor
Authors: Sakurai Yoshiko , Arai Ken‐ichi , Watanabe Sumiko 
Published: March 2003

The granulocyte‐macrophage colony‐stimulating factor (GM‐CSF) receptor activates multiple and complex signalling pathways in response to GM‐CSF stimulation. Biochemical studies suggested that signalling pathways are transmitted through protein/protein interactions, but how these biochemical cascades are initiated and transmitted in response to cytokine stimulation is largely unknown.To investigate these events biochemically, we established an in vitro system leading to the GM‐CSF‐dependent activation of Janus kinase (JAK) 2/signal transducer and activator of transcription (STAT) 5 in cell homogenates prepared from BA/F3 cells expressing the GM‐CSF receptor. Activation of STAT5 DNA binding ability requires both membrane and cytoplasmic fractions while phosphorylation of JAK2 requires only the membrane fraction. Since the addition of anti‐βc or phosphotyrosine antibodies inhibited GM‐CSF induced STAT5 DNA binding activity, we examined the role of tyrosine residues of βc for in vitro activation of STAT5. Addition of synthetic tyrosine‐phosphorylated peptides derived from βc cytoplasmic tyrosines prior to GM‐CSF stimulation inhibited the in vitro activation of STAT5. The association between these tyrosine‐phosphorylated peptides and STAT5 was observed by using peptide‐coupling beads and BA/F3 lysates.We established a GM‐CSF‐dependent in vitro system. In cases of STAT5 activation, each phosphorylated tyrosine residue of βc can act as a docking site and enhance STAT5 activation.
Induction of IRF‐3/‐7 kinase and NF‐κB in response to double‐stranded RNA and virus infection: common and unique pathways
Authors: Iwamura Tomokatsu , Yoneyama Mitsutoshi , Yamaguchi Kazumi , Suhara Wakako , Mori Wakana , Shiota Kazutaka , Okabe Yasutaka , Namiki Hideo , Fujita Takashi 
Published: March 2003

BackgroundsInfection by virus or treatment with double‐stranded RNA (dsRNA) results in the activation of transcription factors including IRF‐3, IRF‐7 and a pleiotropic regulator NF‐κB by specific phosphorylation. These factors are important in triggering a cascade of antiviral responses. A protein kinase that is yet to be identified is responsible for the activation of these factors and plays a key role in the responses.ResultsThe signal cascade was analysed using sensitive assays for the activation of IRF‐3 and NF‐κB, and various inhibitors. We found that the activation of IRF‐3 and NF‐κB by dsRNA or virus involves a process that is sensitive to Geldanamycin. Although the induction of NF‐κB by dsRNA/virus and TNF‐α involves common downstream pathways including IKK activation, the upstream, Geldanamycin‐sensitive process was unique to the dsRNA/virus‐induced signal. By an in vitro assay using cell extract, we found an inducible protein kinase activity with physiological specificity of IRF‐3 phosphorylation. Furthermore, the same extract specifically phosphorylated IRF‐7 in a similar manner.ConclusionsDouble‐stranded RNA or virus triggers a specific signal cascade that results in the activation of the IRF‐3/‐7 kinase we detected, which corresponds to the long‐sought signalling machinery that is responsible for triggering the early phase of innate response. The signal branches to a common NF‐κB activation cascade, thus resulting in the activation of a set of critical transcription factors for the response.
Identification of the cis‐acting region in the NF2 gene promoter as a potential target for mutation and methylation‐dependent silencing in schwannoma
Authors: Kino Takeshi , Takeshima Hideo , Nakao Mitsuyoshi , Nishi Toru , Yamamoto Keizo , Kimura Takahiro , Saito Yoshiki , Kochi Masato , Kuratsu Jun‐ichi , Saya Hideyuki , Ushio Yukitaka 
Published: March 2003

BackgroundAlthough mutational inactivation and allelic loss in the NF2 gene appear to be causal events in the majority of vestibular schwannomas, involvement of another potentially important mechanism, transcriptional inactivation, has not been investigated.ResultsWe cloned and functionally characterized the 5′‐flanking region of the human NF2 gene and identified the molecular mechanisms that regulate NF2 expression. Luciferase assay and site‐directed mutagenesis demonstrated that a 70‐base pair (bp) region (−591 to −522 bp from the translation start site) was essential for the basic expression of the NF2 gene. A gel mobility shift assay indicated recognition by nuclear protein of the unusually long (≈66 bp) sequences in this region. Recognition was inhibited by either mutation of the binding core sequence or by methylation of three CpG sites. Point mutations at these CpG sites significantly decreased promoter activity, suggesting the importance of these sites. In 14 of 23 vestibular schwannomas, these three CpG sites were methylated in a site‐specific manner and the methylation status was consistent with the expression of NF2 mRNA.ConclusionSuppressed expression by aberrant methylation or mutation of the promoter elements could be an alternative mechanism for inactivation of the NF2 gene.
Detection of tmRNA‐mediated trans‐translation products in Bacillus subtilis
Authors: Fujihara Ai , Tomatsu Hisashi , Inagaki Sachi , Tadaki Toshimasa , Ushida Chisato , Himeno Hyouta , Muto Akira 
Published: March 2003

AbstractBackground:Bacterial tmRNA (10Sa RNA) is involved in a trans‐translation reaction, which contributes to the degradation of incompletely synthesized peptides and the recycling of stalled ribosomes. To investigate the physiological roles of this reaction in Bacillus subtilis, we devised a system for detecting the proteins that are subject to in vivo trans‐translation.Results: The wild‐type tmRNA gene (ssrA) in the genome was replaced by a variant ssrA encoding a tag‐peptide sequence containing six histidine residues (His‐tag) and two aspartic acids at the C‐terminus. The His‐tagged proteins that accumulated in the cells without degradation were fractionated by Ni2+‐NTA column and gel electrophoresis and were detected by Western blotting with an anti‐His‐tag antibody. The results showed that the trans‐translation occurred more frequently at a high temperature (50 °C) than at a low temperature (37 °C). Two‐dimensional (2D) gel electrophoresis of the products revealed many distinct spots, which represent specific target proteins for the trans‐translation reaction. Furthermore, the 2D gel patterns of the products from cells cultured at high and low temperatures were apparently different. Several tagged proteins were identified by the N‐terminal amino acid sequences of the products.Conclusion: Trans‐translation occurs more frequently at high temperature than at low temperature, and different proteins are tagged at different temperatures.
The γ‐tubulin complex protein Alp4 provides a link between the metaphase checkpoint and cytokinesis in fission yeast
Authors: Vardy Leah , Fujita Akiko , Toda Takashi 
Published: March 2003

AbstractBackground:  The progression of cytokinesis requires cyclin B destruction by the anaphase promoting complex (APC/C) and, in fission yeast, activation of the septation initiation network (SIN) is also essential. The γ‐tubulin complex (γ‐TuC) localizes to the centrosome throughout the cell cycle and is directly involved in the organization of the mitotic spindle.Results:  We have previously shown that the mutant defective in alp4+ (Spc97/GCP2) displays bipolar spindle defects due to a failure in the recruitment of the γ‐TuC on to the spindle pole body (SPB, the centrosome equivalent). Here we show that in these mutants the Mad2 checkpoint is activated, yet septation proceeds due to the untimely activation of the SIN. The Sid1 kinase, the downstream effector of the SIN, is recruited prematurely to both, instead of only one, of the SPBs, which triggers septation despite the presence of monopolar spindles. Remarkably, cyclin B levels, which would normally have declined, remain high at the SPB in septated mutant cells.Conclusions:  We propose a novel role of the γ‐TuC in inhibiting activation of the SIN until cyclin B is destroyed. Given the ubiquitous existence of the γ‐TuC, this mechanism may be conserved throughout evolution and function to couple cytokinesis to mitotic exit.
Gene products encoded in the ninR region of phage λ participate in Red‐mediated recombination
Authors: Tarkowski Trudee A. , Mooney Duane , Thomason Lynn C. , Stahl Franklin W. 
Published: March 2003

AbstractBackground:  The ninR region of phage λ contains two recombination genes, orf (ninB) and rap (ninG), that were previously shown to have roles when the RecF and RecBCD recombination pathways of E. coli, respectively, operate on phage λ.Results:  When λ DNA replication is blocked, recombination is focused at the termini of the virion chromosome. Deletion of the ninR region of λ decreases the sharpness of the focusing without diminishing the overall rate of recombination. The phenotype is accounted for in large part by the deletion of rap and of orf. Mutation of the recJ gene of the host partially suppresses the Rap– phenotype.Conclusion: ninR functions Orf and Rap participate in Red recombination, the primary pathway operating when wild‐type λ grows lytically in rec+ cells. The ability of recJ mutation to suppress the Rap– phenotype indicates that RecJ exonuclease can participate in Red‐mediated recombination, at least in the absence of Rap function. A model is presented for Red‐mediated RecA‐dependent recombination that includes these newly identified participants.