bluuebunny/crossref_metadata_2025_split huggingface dataset:
Why are species’ body size distributions usually skewed to the right?
Authors: Kozłowski Jan , Gawelczyk Adam. T. 
Published: March 2003

Summary1. Species’ body size distributions are right‐skewed, symmetric or left‐skewed, but right‐skewness strongly prevails.2. Skewness changes with taxonomic level, with a tendency to high right‐skewness in classes and diverse skewness in orders within a class. Where the number of lower taxa allows for analysis, skewness coefficients have normal distributions, with the majority of taxa being right‐skewed.3. Skewness changes with geographical scale. For a broad range, distributions in a class are usually right‐skewed. For a narrower scale, distributions remain right‐skewed or become symmetric or even close to uniform.4. The prevailing right‐skewness of species’ body size distributions is explained with macroevolutionary models, the fractal character of the environment, or body size optimization.5. Macroevolutionary models assume either size‐biased speciation and extinction, or the existence of a constraint on small size. Macroevolutionary mechanisms seem insufficient to explain the pattern of species’ body size distributions, but they may operate together with other mechanisms.6. Optimization models assume that directional and then stabilizing selection works after speciation events. There are two kinds of optimization approaches to study species’ body size distributions. Under the first approach, it is assumed that a single energetic optimum exists for an entire taxon, and that species are distributed around this optimum. Under the second approach, each species has a separate optimum, and the species’ body size distribution reflects the distribution of optimal values.7. Because not only energetic properties but also mortality are important in determining optimal sizes, only the second approach, that is, seeking the distribution of optimal values, seems appropriate in the context of life‐history evolution. This approach predicts diverse shapes of body size distributions, with right‐skewness prevailing.
Assembly rules and functional groups at global biogeographical scales
Authors: Bellwood D. R. , Wainwright P. C. , Fulton C. J. , Hoey A. 
Published: March 2003

Summary

The taxonomic and functional composition of reef fish assemblages are quantified in three biogeographical regions: Great Barrier Reef, French Polynesia and Caribbean. Assemblages are described in three habitats of differing wave exposure. Functional abilities are estimated based on published analyses linking fin morphology and swimming performance.
Two questions were addressed: (1) To what extent are labrid assemblages similar among habitats and regions? (2) To what extent are functional characteristics of fish assemblages shaped by differences in biodiversity, evolutionary history and species composition?
All three regions display highly congruent patterns of habitat use, in terms of assemblage structure and functional characteristics, despite a five‐fold difference in species richness, limited or no species overlap, and a 3·2‐Myear history of isolation. Exposed reef crest assemblages were dominated by fishes with fins reflecting lift‐based high‐speed locomotion. In contrast to abundance‐based patterns, species presence/absence data were uninformative.
The relationship between swimming ability and habitat use reveals underlying assembly rules at a functional level, emphasizing the utility of functional attributes as a metric for comparing system‐level properties in taxonomically distinct faunas.
Nutritional stress changes sex‐specific reproductive allocation in the simultaneously hermaphroditic land snailArianta arbustorum
Authors: Locher R. , Baur B. 
Published: March 2003

SummarySex allocation theory predicts that when resources are limited in simultaneous hermaphrodites, the allocation to one sexual function will automatically reduce the resources available to the other function. This study examines the effect of nutritional stress on mating behaviour and male and female reproductive output (dry mass and nitrogen contents of spermatophores, sperm delivered and eggs deposited) in individuals of the simultaneously hermaphroditic land snailArianta arbustorumkept under three different food regimes: ample (100%), restricted (50%) and extremely restricted (25%) food supply.Independent of the extent of nutritional stress, 10–12% of the resources taken up were invested in reproductive output (both gender functions together) and 88–90% in maintenance (including faeces and excretion).Courtship and copulation behaviour was affected by nutritional stress. Snails with an extremely restricted food supply did not mate, except one pair. Individuals with restricted food supply tended to court longer, and copulated for a shorter period, than individuals with ample food supply.Nutritional stress did not affect the number of sperm delivered. However, snails with a restricted food supply produced fewer eggs. Thus, snails kept under nutritional stress invested relatively more resources in the male function than in the female function. Nevertheless, the absolute reproductive output remained highly female biased (>95% in all experimental groups).At the individual level, the existence of a trade‐off between resources invested in the malevsthe female function could not be confirmed. However, there was a trade‐off between nitrogen allocated to reproductive function and maintenance in snails with a restricted food supply.
Passage through bird guts increases germination rate and seedling growth inSorbus aucuparia
Authors: Paulsen T. R. , Högstedt G. 
Published: March 2003

SummaryOn the west coast of Norway,Turdusspp. (Thrushes) are important dispersal agents ofSorbus aucupariaL. (Rowan) seeds, and avian and mammalian gut treatment often alters seed germination characteristics. In the present study the effects of avian gut treatment onS. aucupariaseeds are described, with emphasis on subsequent seedling growth.Seeds ingested byTurdusspp. and non‐ingested control seeds were sown singly or multiply in soil, in pomes, or in bird droppings.Defecated seeds were ≈9% heavier than control seeds, and seedling growth was faster from defecated seeds than controls. In addition, differences in the rate of seedling emergence were found, with seedlings from ingested seeds appearing first.The increased growth may be due to seedlings emerging earlier from defecated seeds, giving them an extended growth period at a time of increasing day length.We argue that factors such as seedling growth, rate of seedling emergence and seed mass, in addition to percentage seed germination, are important in determining seedling survival.
Energy requirements of female Macaroni Penguins breeding at South Georgia
Authors: Green J. A. , Butler P. J. , Woakes A. J. , Boyd I. L. 
Published: March 2003

Summary

Breeding female Macaroni Penguins (Eudyptes chrysolophus) were implanted with heart rate, temperature and depth data loggers in order to estimate their rate of energy expenditure from heart rate.
The estimated average daily metabolic rates (ADMR) of birds during the brood and crèche phases of the breeding season were 8·17 ± 0·44 W kg−1 and 8·24 ± 0·41 W kg−1, respectively. There was no significant difference between these estimates and the pooled ADMR for all birds was 8·22 ± 0·38 W kg−1.
Metabolic rate while the penguins were at‐sea was 9·03 ± 0·39 W kg−1 and this was significantly greater than the metabolic rate of 6·27 ± 0·38 W kg−1 while they were on‐shore.
Females undertook shorter foraging trips during the crèche phase than during the brood phase.
When considered as a breeding pair, Macaroni Penguins expend more energy in raising their chick during the crèche phase of the breeding season as the male assists in provisioning the chick only at this time.
A new mammalian period gene predominantly expressed in the suprachiasmatic nucleus
Authors: Takumi Toru , Matsubara Chiaki , Shigeyoshi Yasufumi , Taguchi Kouji , Yagita Kazuhiro , Maebayashi Yoshiro , Sakakida Yoko , Okumura Ko , Takashima Naoyuki , Okamura Hitoshi 
Published: March 2003

BackgroundIn mammals, two possible clock genes (Clock, Per1) have very recently been reported. mPer1 (the first identified mouse period gene), in particular, shows a circadian expression in suprachiasmatic nuclei (SCN), the mammalian circadian centre. However, only mPer1 and Clock as clock components may not be sufficient to understand all the events in circadian oscillation and entrainment.ResultsA mammalian period complementary DNA, mPer2, has been isolated from the mouse brain. The amino acid sequence of mPer2 is similar to mPer1 and Drosophila Period (dPer), indicating that mPer2 is a member of the family which contains mPer1, itself a homologue of dPer. mPer2 mRNA is predominantly expressed in SCN. A robust circadian rhythmic expression in the SCN supports the view that mPer2 is a clock gene. mPer2 is strongly expressed at the subjective afternoon in constant darkness, distinct from a morning‐phase clock mPer1. Our precise quantitative in situ hybridizations have revealed that the peak expression of mPer2 transcripts is delayed by 8 h in LD (light–dark) or 4 h in DD (dark–dark) conditions when compared to mPer1. A short brief light exposure at the early subjective night, prompting a phase‐shift in locomotor rhythms, induces a transient increase of mPer2 transcripts with delayed onset, as compared to mPer1 mRNA induction. Furthermore, mPer2 is co‐expressed with mPer1 in single SCN cells.ConclusionsMammalian period genes show molecular heterogeneity, each of which is composed of a different oscillator, and may serve to establish stable circadian rhythms in mammalian oscillating cells.
Fas‐induced DNA fragmentation and proteolysis of nuclear proteins
Authors: Kawahara Atsuo , Enari Masato , Talanian Robert V. , Wong Winnie W. , Nagata Shigekazu 
Published: March 2003

BackgroundFas is a member of the tumour necrosis factor (TNF) receptor family. Activation of Fas by its ligand or an agonistic anti‐Fas antibody causes apoptosis in Fas‐bearing cells, by activating various members of the caspase family.ResultsSpecific fluorogenic substrates (MCA‐DEVDAPK[dnp] and MCA‐VEVDAPK[dnp]) for caspases 3 and 6 were prepared. Using these substrates, a gradual increase of the caspase 3‐ and 6‐like proteases were detected during the Fas engagement in human Jurkat. This activation of caspases correlated well with the cleavage of poly(ADP‐ribose) polymerase and lamin B1, as well as with DNA fragmentation. When the recombinant caspases were added to the extracts from Jurkat cells, caspase 3 produced active caspase 6‐like protease, while caspase 6 activated the caspase 3 protease, suggesting that these proteases can activate each other. The caspase‐treated cell extracts, as well as the extracts from the Fas‐activated cells, caused the proteolysis of nuclear proteins and DNA degradation. The cleavage of nuclear proteins was inhibited by caspase inhibitors, while the same inhibitors had no effect on DNA degradation.ConclusionsAt one stage of the caspase cascade, caspases activate each other, and amplify the apoptotic signal. Caspases downstream of the cascade then cause the proteolysis of nuclear proteins and DNA degradation.
Meiotic behaviours of chromosomes and microtubules in budding yeast: relocalization of centromeres and telomeres during meiotic prophase
Authors: Hayashi Aki , Ogawa Hideyuki , Kohno Kenji , Gasser Susan M. , Hiraoka Yasushi 
Published: March 2003

Background" Meiosis is a process of universal importance in eukaryotic organisms, generating variation in the heritable haploid genome by recombination and re‐assortment of chromosomes. The intranuclear movement of chromosomes is expected to achieve pairing and recombination of homologous chromosomes during meiosis. Meiosis in the budding yeast Saccharomyces cerevisiae has been extensively studied, both genetically and by molecular biology; here we report cytological observations of meiotic chromosomal events in this organism.ResultsUsing fluorescence microscopy, we have examined the behaviour of chromosomes and microtubules during meiosis in S. cerevisiae. We first observed the dynamic behaviour of nuclei in living cells using jellyfish green fluorescent protein (GFP) fused with nucleoplasmin, a Xenopus oocyte nuclear protein. The characterization of nuclear movement in living cells was extended by an analysis of chromosomes and microtubules in fixed specimens. In addition, the nuclear localization of centromeres and telomeres was determined by indirect immunofluorescence microscopy in synchronous populations of meiotic cells. While telomeres remain in clusters of 5–8 throughout meiosis, centromeres change their nuclear localization dramatically during the progression of meiosis: centromeres are first clustered at a single site near the spindle‐pole body before the induction of meiosis, and become scattered during the meiotic prophase.ConclusionsOur observations have demonstrated that nuclear and cytoskeletal reorganization take place with meiosis in S. cerevisiae. In particular, the distinct relocalization of centromeres during meiosis indicates a considerable movement of chromosomes within the meiotic prophase nucleus.
Function in vivo of separate segments of the β subunit of Escherichia coli RNA polymerase
Authors: Trigwell Susan , Glass Robert E. 
Published: March 2003

Background:Transcription of genetic material is catalysed by the enzyme DNA‐dependent, RNA polymerase. The multimeric RNA polymerases consist of between 4 and 16 different subunits, of which the two largest, termed β and β′, are conserved throughout nature. The β subunit has been implicated in all of the stages of transcription that are catalysed by the complete enzyme. Several lines of evidence have suggested that the function of the β subunit is not dependent upon the contiguity of the sequence blocks. In this report, a complementary immunological and genetic approach was adopted in order to investigate the individual regions of the β subunit of RNA polymerase. To this end, the β structural gene rpoB was separated into four near‐equal, non‐overlapping segments (as well as ‘half’ genes) on the basis of ‘split’ genes in nature, known functional organization and sequence conservation. These segments were used to prepare sequence‐specific antibodies against the four individual regions, as well as being expressed in vivo from a tight, lac‐controlled high‐copy number vector.Results:Immunological probing of the holoenzyme in vitro suggested that the amino‐terminal half of the β polypeptide is buried within the enzyme complex. Of the four segments expressed in vivo, the extreme C‐terminal segment was trans‐dominant lethal (of the effect of large N‐terminal amber fragments on cellular growth; Nene & Glass 1982) and this isolated region was shown to bind the translational elongation factor EF‐Tu in vivo.Conclusions:These in vivo and in vitro studies, in conjunction with recent in vitro work (Severinov et al. 1995), unambiguously demonstrate that individual regions of β may adopt structurally and functionally competent forms, and underline the possibility of in vivo investigation of separate regions of this massive polypeptide chain. A model is presented for the role of EF‐Tu in stringent control.
Two F‐box/WD‐repeat proteins Pop1 and Pop2 form hetero‐ and homo‐complexes together with cullin‐1 in the fission yeast SCF (Skp1‐Cullin‐1‐F‐box) ubiquitin ligase
Authors: Kominami Kin‐ichiro , Ochotorena Itziar , Toda Takashi 
Published: March 2003

Background:In the ubiquitin‐dependent proteolysis pathway, a ubiquitin ligase (E3) is responsible for substrate selectivity and timing of degradation. A novel E3, SCF (Skp1‐Cullin‐1/Cdc53‐F‐box) plays a pivotal role in cell cycle progression. In fission yeast, F‐box/WD‐repeat protein Pop1 regulates the level of the CDK (cyclin‐dependent kinase) inhibitor Rum1 and the S phase regulator Cdc18.Results:We have cloned and characterized the pop2+ gene which encodes the Pop1‐related F‐box/WD‐repeat protein. Pop2 plays a role which overlaps with Pop1 in the degradation of Rum1 and Cdc18. However, these two proteins are not functional homologues. Pop1 and Pop2 form hetero‐ as well as homo‐dimers in the cell. We have analysed two fission yeast cullin members and found that cullin‐1 functions as a component of SCFPop1,2, whilst cullin‐3 is involved in the distinct stress‐response pathway.Conclusions:Fission yeast SCF is composed of Pop1 and Pop2, two structurally related but functionally independent F‐box/WD‐repeat proteins. By forming three distinct complexes, SCFPop1/Pop1, SCFPop1/Pop2 and SCFPop2/Pop2, SCF has evolved a sophisticated mechanism to control the level of Rum1 and Cdc18. Fission yeast SCF also contains cullin‐1 as a universal scaffold and each cullin member plays a distinct biological role.
Impaired extrapyramidal function caused by the targeted disruption of Retinoid X receptor RXRγ1 isoform
Authors: Saga Yumiko , Kobayashi Masahiko , Ohta Hisashi , Murai Naomi , Nakai Nami , Oshima Masanobu , Taketo Makoto M. 
Published: March 2003

BackgroundRetinoid X receptors RXRα, β and γ exert multiple functions in the genetic regulation of mammalian signalling systems by forming heterodimeric complexes with several nuclear ligand receptors. In contrast to the widespread expression of RXRα and RXRβ, the expression of RXRγ is restricted to particular tissues in which RXRγ1 is the major isoform expressed in the mouse corpus striatum.ResultsTo investigate the function of this particular isoform RXRγ1, we generated RXRγ1 gene‐knockout mice by homologous recombination in ES cells. Both heterozygous and homozygous mice showed severe runting after birth, which often resulted in the early death of mice of the 129/C57BL‐6 genetic background. Independent of genetic background, however, the expression of choline acetyltransferase (ChAT) in the cholinergic interneurones in the striatum (caudal putamen) was markedly reduced in the RXRγ1 gene‐null mice. Furthermore, the mutant exhibited an altered response to the administration of dopamine receptor antagonists, haloperidol and chlorpromazine, which normally induce catalepsy in mice.ConclusionsThese results strongly suggest that RXRγ1 plays an important role in either the development or activation of cholinergic neurones in nigrostriatal extrapyramidal pathways.
The G10BP‐1 gene encoding a GC box binding protein, is a target of Myc and Jun/Fos
Authors: Shirasuna Kenna , Takeuchi Arata , Bando Takayoshi , Nakajima Takuma , Oda Kinichiro 
Published: March 2003

BackgroundG10BP, a serum‐inducible factor, represses the transcription of the fibronectin gene through binding to the G‐rich sequences in the promoter excluding Sp1 from binding to these sequences.ResultsThe 5′ flanking sequence of the G10BP‐1 gene was isolated by polymerase chain reaction of the adaptor‐ligated genomic DNA library using the adaptor primer and the G10BP‐1 cDNA primer. The elements required for activation of the G10BP‐1 promoter following serum stimulation were analysed by transfection of quiescent rat 3Y1 cells with G10BP‐1 promoter‐luciferase cDNA constructs containing 5′ sequential deletions or base substitutions. The results showed that the promoter was activated by Myc and Jun through the E box and AP1 sites. The formation of DNA–protein complexes with 32P‐labelled oligonucleotides containing the E box or AP1 site with cell extracts prepared during G1 progression was correlated with the promoter activation and greatly reduced by immunodepletion of Myc or c‐Jun from the extracts.ConclusionThese results indicate that the G10BP‐1 gene is a target of Myc and Jun/Fos and that these factors repress the fibronectin gene expression through induction of G10BP‐1 during G1‐to‐S phase progression.
Amber (UAG) suppressors affected in UGA/UAA‐specific polypeptide release factor 2 of bacteria: genetic prediction of initial binding to ribosome preceding stop codon recognition
Authors: Yoshimura Kuniyasu , Ito Koichi , Nakamura Yoshikazu 
Published: March 2003

BackgroundProkaryotic translational release factors, RF1 and RF2, catalyse protein release at UAG/UAA and UGA/UAA stop codons, respectively. Mutations in RF1 and RF2 are known to cause non‐sense suppression for UAG (amber) and UGA (opal) codons, respectively, and they do not exert a reciprocal (‘cross’) suppression phenotype. We aimed to isolate RF mutants of such cross‐suppression activity, which we designated ‘Csu’ phenotype in this paper.ResultsUsing a lacZ (UAG) reporter, we selected amber suppressor alleles occurring in the plasmid‐bearing RF2 gene of Salmonella typhimurium. Of nine such RF2 csu alleles, five were mis‐sense mutations and four were non‐sense mutations. The former mis‐sense mutants retained the RF2 activity and catalysed UGA termination both in vivo and in vitro. RF2 C‐terminal deletions equivalent to the non‐sense alleles exerted amber suppression as well as opal suppression activity. Moreover, the equivalent RF1 segments also showed both the suppression phenotypes.ConclusionsAll the csu mutations were mapped at the C‐terminal half of RF2 and are strikingly coincident with the highly conservative amino acids, suggesting that they affect the conserved function of bacterial RFs. We propose here that there should be an ‘initial binding’ step of RFs to the ribosome, preceding stop codon recognition (‘initial binding’ hypothesis) and that the N‐terminal RF domain(s), that are truncated or affected by the csu mutations, are responsible for this step and interfere with the proper functioning of cognate release factors on the ribosome.
Critical role of the membrane‐proximal, proline‐rich motif of the interleukin‐2 receptor γc chain in the Jak3‐independent signal transduction
Authors: Tsujino Shiho , Miyazaki Tadaaki , Kawahara Atsuo , Maeda Michiyuki , Taniguchi Tadatsugu , Fujii Hodaka 
Published: March 2003

BackgroundThe interleukin‐2 receptor (IL‐2R) consists of three subunits, the IL‐2Rα, IL‐2Rβc, and IL‐2Rγc chains. The essential role of the IL‐2Rγc cytoplasmic domain, consisting of 86 amino acids, in signal transmission has been well documented. Particularly, the carboxyl ter‐minal region containing 48 amino acids. is essential for the association with and activation of the Jak3 protein tyrosine kinase. On the other hand, little is known about the role of the rest of the IL‐2Rγc cytoplasmic region consisting of the membrane‐proximal 38 amino acids.ResultsWe show that a truncated mutant form of IL‐2Rγc which lacks the membrane‐distal 48 amino acids is still capable of inducing the activation of Jak1 and Stat3/Stat5 in the absence of Jak3 activation. This membrane‐proximal region can also mediate the IL‐2‐induced tyrosine phosphorylation of the p85 subunit of phosphatidylinositol‐3‐kinase (PI3K). Furthermore, these signalling events are completely abrogated when mutations are introduced into the proline‐rich motif in this region.ConclusionsIn this study, we identified a Jak3‐independent signalling pathway(s) from the membrane‐proximal region of IL‐2Rγc. Our results indicate that the proline‐rich motif in this region plays a critical role in this signalling pathway(s). The present study may provide further insight into the mechanism of cellular responses mediated by IL‐2 and other cytokines which utilize the IL‐2Rγc for their signal transmission.