bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of a generalised linear model to test habitat preferences: the example of Zingel asper, an endemic endangered percid of the River Rhône
Authors: Labonne Jacques , Allouche Stephanie , Gaudin Philippe 
Published: July 2003

SUMMARY 1. A study of microhabitat preferences was conducted on Zingel asper, an endangered endemic species from the Rhône catchment. A generalised linear model allowed us to test statistically the non‐random habitat selection and the effect of season and site on this habitat selection.2. The analysis detected significant preferences for the three physical variables considered: water depth, water velocity and substratum size.3. A seasonal shift in the substratum size preference was found: preference for stones increasing during the spawning season. Depth preference varied between sites, suggesting a possible plasticity in habitat selection.4. These results suggest that the availability of suitable physical habitat plays a significant role in determining fish distribution in the River Beaume.
Quantitative trait loci conditioning transovarial transmission of La Crosse virus in the eastern treehole mosquito, Ochlerotatus triseriatus
Authors: Graham Douglas H. , Holmes Jennifer L. , Beaty Barry J. , Black William C. 
Published: July 2003

AbstractQuantitative trait loci (QTL) affecting the ability of the Eastern treehole mosquito, Ochlerotatus triseriatus, to transovarially transmit (TOT) La Crosse virus (LAC) were mapped in an F1 intercross. The Holmen strain of O. triseriatus, previously selected for TOT refractoriness, was crossed to the AIDL strain that had been selected for TOT permissiveness. In P1 and F1 parents and 49 F2 individuals, regions of 10 cDNA loci were analysed with single strand conformation polymorphism (SSCP) analysis to identify and orientate linkage groups. Genotypes were also scored at fifty‐six random amplified polymorphic DNA (RAPD)‐SSCP loci. Twenty‐eight F2 offspring were individually analysed for TOT. Three QTL for TOT were detected with standard interval mapping on chromosomes II and III. Alleles at the three loci contributed additively towards determining the overall TOT rate and cumulatively accounted for ≈ 53% of the phenotypic variance in TOT.
Expression of an Aedes aegypti cation‐chloride cotransporter and its Drosophila homologues
Authors: Filippov V. , Aimanova K. , Gill S. S. 
Published: July 2003

AbstractInsects maintain haemolymph homeostasis under different environmental conditions by modulating the concentrations of Na+, K+ and Cl– ions. One group of proteins involved in ion transport across cell membranes consists of cation‐chloride cotransporters that form a family of structurally similar proteins. Although much is known about these proteins in mammalian systems, our understanding of them in insects is lacking. The recent sequencing of two insect genomes, Drosophila and Anopheles, enabled us to identify globally members of the family of cation chloride cotransporters in these insects. Using RT‐PCR we monitored the transcription of members of this family in development and in several tissues. Our analyses showed that transcription of these genes differ considerably from the ubiquitously and highly expressed CG5594 gene to the almost silent gene CG31547. Comparison of Drosophila CG12773 and its Aedes homologue AaeCG12773 showed that they have similar transcript expression profiles. Immunohistochemical analysis of AaeCG1277 gene expression revealed that it is highly expressed in the gut of larvae and female adults but not in Malpighian tubules. A more detailed analysis showed that this protein is localized predominantly in the basolateral membrane of these tissues. This expression pattern confirmed the results of RT‐PCR analysis. We also created a mutant for one of the genes, CG10413, in Drosophila using P‐element excision. Analysis of this mutant showed this protein does not appear to be essential for development.
The AmCREB gene is an ortholog of the mammalian CREB/CREM family of transcription factors and encodes several splice variants in the honeybee brain
Authors: Eisenhardt D. , Friedrich A. , Stollhoff N. , Müller U. , Kress H. , Menzel R. 
Published: July 2003

AbstractThe transcription factor CREB (cAMP response element binding protein) is required for the switch from short‐term to long‐term synaptic plasticity and from short‐term to long‐term memory. Its activity is regulated by the cAMP‐dependent signalling cascade, which has been shown to play a crucial role in the honeybee's long‐term memory formation. To elucidate the role of the CREB in honeybee memory formation we analysed a CREB‐homologous gene, AmCREB, which is expressed as several transcripts in the honeybee brain. Eight transcripts have been identified (AmCREB 1–8) that are generated by alternate splicing. One antibody generated against a subset of these variants reveals a cytosolic localization in the mushroom body α‐lobes, the glomeruli of the antennal lobes, the protocerebral lobes, the central complex and in the optical lobes.
Transcriptome analysis of the cowpea weevil bruchid: identification of putative proteinases and α‐amylases associated with food breakdown
Authors: Pedra J. H. F. , Brandt A. , Westerman R. , Lobo N. , Li H.‐M. , Romero‐Severson J. , Murdock L. L. , Pittendrigh B. R. 
Published: July 2003

AbstractWe describe here the first systematic work to discover insect genes involved in food breakdown using a cDNA library enriched for gut‐expressed transcripts from Callosobruchus maculatus. A total of 1056 clones were screened for cDNA insert‐containing plasmids, and 503 nonredundant open reading frames were discovered. Twenty‐three inferred genes potentially involved in digestive processes in cowpea weevil were identified, including proteinases and amylases. The predicted catalytic sites were identified in the inferred cysteine and aspartic acid proteinases, and in α‐amylases. Transcriptome analysis of the cowpea bruchid will potentially permit gene discovery in other beetles, an insect order of major economic and ecological importance that is poorly represented in genomic databases.
Effects of refuge availability on the population dynamics ofTriatoma infestansin central Argentina
Authors: Cecere Maria C. , Canale Delmi M. , Gürtler Ricardo E. 
Published: July 2003

SummaryAs part of research on the control and mathematical modelling of transmission of Chagas disease, we tested the joint effects of refuge quantity and quality on the population dynamics ofTriatoma infestansin 12 experimental huts under natural climatic conditions in central Argentina.The 2‐year trial involved three types of huts that mimicked rural houses, with a gradient of refuges determined by the type of thatched roof and whether the walls were plastered or not. Each treatment comprised three replicate huts and one control hut, each of which was a closed population that housed a chicken at night and was colonized with five virgin female and three maleT. infestansin mid‐summer. The replicate huts were dismantled monthly to count the number of live and deadT. infestansby stage and to mark the emerged insects. Control huts were dismantled only at the end of the first and second year to count the bugs.The mean abundance of liveT. infestanswas significantly greater in huts with maximum (final mean 1834; range 337–3630 bugs) rather than intermediate (final mean 383; range 71–692 bugs) or minimum refuges (final mean 103; range 0–103 bugs). The bug populations under minimum refuges returned to baseline levels at 1 year post‐colonization and two populations went extinct.Apparent female fecundity was affected significantly by refuge availability and time. Survival of the founder females until 1 year post‐colonization successively decreased from 20% to 7% and 0% in huts ranging from maximum to minimum refuges. The basic reproduction number Rosteadily decreased from 3·91 to 2·36–0·25 bugs per female bug in maximum to minimum refuge huts, respectively.Synthesis and applications. Population persistence, growth rate and the maximum number ofT. infestansthat a hut may support depend on the physical structure for a fixed number of chickens, in agreement with the available experimental and field evidence. Environmental management measures, such as plastering of walls and wire‐fencing corrals, aimed at reducing the availability of refuges and oviposition sites may exert a strong adverse impact on the population dynamics ofT. infestans.
Foraging by bats in cleared, thinned and unharvested boreal forest
Authors: Patriquin Krista J. , Barclay Robert M. R. 
Published: July 2003

SummaryModern silvicultural methods employ various styles of selective harvesting in addition to traditional clear‐cutting. This can create a mosaic of patches with different tree densities that may influence habitat use by foraging bats. Use of forest patches may also vary among bat species due to variation in their manoeuvrability. Apart from studies investigating use of clear‐cuts, few have tested for differences in use of forest patches by bats, or for differences among bat species.We investigated the influence of various harvesting regimes, which created forest patches of different tree densities, on habitat selection by foraging bats in the boreal mixed‐wood forest of Alberta, Canada. We also tested for variation in habitat selection among species related to differences in body size and wing morphology.Over two summers we assessed habitat use by bats using ultrasonic detectors to count the echolocation passes of foraging bats. We measured activity in three forest types and four tree densities, ranging from intact (unharvested) forests to clear‐cuts.Smaller, more manoeuvrable, species (Myotisspp.) were less affected by tree density than the larger, less manoeuvrable,Lasionycteris noctivagans. TwoMyotisspp. differed in their habitat use.Myotis lucifugus, an aerial insectivore, preferred to forage along the edge of clear‐cuts, whileM. septentrionalis, a species that gleans prey from surfaces, did not forage in clear‐cuts but preferred intact forest.The largest species in our study,L. noctivagans, preferred clear‐cuts and avoided intact patches. There were therefore differences in habitat selection by foraging bats among the species in our study area, and these were correlated with size and wing morphology.Synthesis and applications. Our results suggest that, in the short term, thinning has minimal effect on habitat use by bats. They also indicate that silvicultural methods have different immediate effects on different species of bats that may be obscured if the community is studied as a single entity. Management for forest‐dwelling bats must take such species‐specific effects into consideration. Harvesting that creates a mosaic of patches with different tree densities is likely to satisfy the requirements of more species than a system with less diverse harvesting styles.
Estimation of badger abundance using faecal DNA typing
Authors: Wilson G. J. , Frantz A. C. , Pope L. C. , Roper T. J. , Burke T. A. , Cheeseman C. L. , Delahay R. J. 
Published: July 2003

Summary

Wildlife management and conservation programmes often require accurate information on population density, but this can be difficult to obtain, particularly when the species in question is nocturnal or cryptic. Badger populations in Britain are of intense management interest because they are a wildlife reservoir host of bovine tuberculosis (TB). Attempts to manage this infection in badgers, whether by population control or vaccination, require reliable methods of estimating population size. In addition, such estimates are also required to support research into badger ecology and TB epidemiology. Currently, the most accurate estimates of local badger population size are obtained from labour‐intensive and time‐consuming mark–recapture studies.
In recent years, DNA has been successfully extracted from the faeces of certain mammals, and used to generate a genetic profile of the defecating individual. Here we report on an application of this technology to estimate badger abundance.
Faecal samples were collected on 10 consecutive days from every freshly deposited dropping at latrine sites close to occupied setts in three badger social groups. Badger DNA was extracted from 89% of samples, and 20 different individuals were reliably identified. The genotypes derived from the faecal samples were compared with those obtained from blood or samples from badgers live trapped at the same setts.
The faecal genotypes from badgers with known trap histories revealed that latrines were used equally by males and females, and by badgers ranging in age from cubs (< 1 year old) to 9 years old. Individual badgers used the latrines on between one and six different nights. Rarefaction analysis produced abundance estimates that closely matched those obtained from live trapping.
Synthesis and applications. Systematic sampling and genetic typing of fresh faeces from badger latrines can provide data that can be used to estimate abundance accurately. This approach requires considerably less human resources than repeated live trapping and mark–recapture. The technique may be valuable for future badger research and management in relation to bovine TB, where accurate estimates of abundance at a local scale are required.
Vegetation dynamics on rangelands: a critique of the current paradigms
Authors: Briske D. D. , Fuhlendorf S. D. , Smeins F. E. 
Published: July 2003

Summary

Rangeland ecologists have been debating the validity of two current paradigms for the evaluation of vegetation dynamics on rangelands. This debate frequently contrasts the conventional model of continuous and reversible vegetation dynamics (range model) with a more contemporary model that can accommodate discontinuous and non‐reversible vegetation change (state‐and‐transition model).
The range and the state‐and‐transition models are conceptually related to the equilibrium and non‐equilibrium paradigms within ecology, respectively. The methodological dichotomy that has developed between the range and the state‐and‐transition models has fostered the perception that these two ecological paradigms are mutually exclusive. We challenge this perception and contend that both methodologies and their corresponding paradigms are non‐exclusive.
Equilibrium and non‐equilibrium ecosystems are not distinguished on the basis of unique processes or functions, but rather by the evaluation of system dynamics at various temporal and spatial scales. Consequently, ecosystems may express both equilibrium and non‐equilibrium dynamics. This confirms early interpretations that ecosystems are distributed along a continuum from equilibrium to non‐equilibrium states.
Although both equilibrium and non‐equilibrium dynamics occur in numerous ecosystems, the empirical evidence is frequently confounded by (i) uncertainty regarding the appropriate evidence necessary to distinguish between paradigms; (ii) disproportionate responses among vegetation attributes to climate and grazing; (iii) comparisons among systems with varying degrees of managerial involvement; and (iv) the evaluation of vegetation dynamics at various spatial and temporal scales.
Synthesis and applications. This critique supports the conclusion that a paradigm shift has not taken place in rangeland ecology, but rather, the debate has forced a more comprehensive interpretation of vegetation dynamics along the entirety of the equilibrium–non‐equilibrium continuum. Therefore, the rangeland debate should be redirected from the dichotomy between paradigms to one of paradigm integration.
IRE1‐ and HAC1‐independent transcriptional regulation in the unfolded protein response of yeast
Authors: Schröder Martin , Clark Robert , Kaufman Randal J. 
Published: July 2003

SummaryThe unfolded protein response (UPR) is a signalling pathway leading to transcriptional activation of genes that protect cells from accumulation of unfolded proteins in the lumen of the endoplasmic reticulum (ER). In yeast, the only known ER stress signalling pathway originates at the type I transmembrane protein kinase/endoribonuclease Ire1p. Ire1p regulates synthesis of the basic leucine‐zipper (bZIP)‐containing transcription factor Hac1p by controlling splicing of HAC1 mRNA. Only spliced HAC1 mRNA (HAC1i) is translated, and Hac1ip activates transcription of genes that contain a conserved UPR element (UPRE) in their promoters. Here, we demonstrate that in addition to this well‐understood ER stress signalling pathway, a second, IRE1, HAC1 and UPRE‐independent mechanism for transcriptional activation upon ER stress, exists in yeast. A genetic screen identified recessive SIN4 alleles as suppressors of a defective UPR in ire1Δ strains. Elevation of basal transcription in sin4 strains or by tethering the RNA polymerase II holoenzyme with LexAp‐holoenzyme component fusion proteins to a promoter allowed for activation of the promoter by ER stress in an IRE1, HAC1 and UPRE‐independent manner. We propose that this novel second ER‐to‐nucleus signal transduction pathway culminates in core promoter activation (CPA) through stimulation of RNA polymerase II holoenzyme activity. Core promoter activation was observed upon diverse cellular stresses, suggesting it represents a primordial stress‐induced gene activation mechanism.
Recovery of adhesion to chondroitin‐4‐sulphate in Plasmodium falciparum var CSA disruption mutants by antigenically similar PfEMP1 variants
Authors: Andrews Katherine T. , Pirrit Lindsay A. , Przyborski Jude M. , Sanchez Cecilia P. , Sterkers Yvon , Ricken Sigrid , Wickert Hannes , Lépolard Catherine , Avril Marion , Scherf Artur , Gysin Jürg , Lanzer Michael 
Published: July 2003

SummaryProtection against maternal malaria has been associated with the acquisition of a specific antibody response that prevents adhesion of Plasmodium falciparum‐infected erythrocytes to the glycosaminoglycan chondroitin‐4‐sulphate (CSA), which is present in the placental intervillous space. These antibodies are directed against variant forms of the P. falciparum erythrocyte membrane protein 1 (PfEMP1) that mediate binding to CSA. We have generated insertional disruption mutants of the gene encoding the CSA‐binding phenotype in the P. falciparum clone FCR3 (var CSA) to test the hypothesis that strategies targeting the parasite's determinant for this adhesive phenotype may prevent sequestration of infected erythrocytes in the placenta and hence the development of maternal malaria. The var CSA‐disruption mutants were initially unable to adhere to CSA; however, they could recover the phenotype after repeated selection over CSA. We show that recovery of CSA binding is var CSA independent and mediated by the activation of a novel var variant. Importantly, the corresponding PfEMP1 protein reacts with a monoclonal antibody recognizing the DBL3γ domain of the var CSA gene product, indicating that the DBL3γ CSA‐binding domains are conserved between these PfEMP1‐binding variants. Our data support strategies exploring these conserved epitopes as vaccine candidates against maternal malaria.
Bacterial shape
Authors: Young Kevin D. 
Published: July 2003

‘Architecture is the adaptation of form to resist force’.John Ruskin (1874)
SummaryIn free‐living eubacteria an external shell of peptidoglycan opposes internal hydrostatic pressure and prevents membrane rupture and death. At the same time, this wall imposes on each cell a shape. Because shape is both stable and heritable, as is the ability of many organisms to execute defined morphological transformations, cells must actively choose from among a large repertoire of available shapes. How they do so has been debated for decades, but recently experiment has begun to catch up with theory. Two discoveries are particularly informative. First, specific protein assemblies, nucleated by FtsZ, MreB or Mbl, appear to act as internal scaffolds that influence cell shape, perhaps by correctly localizing synthetic enzymes. Second, defects in cell shape are correlated with the presence of inappropriately placed, metabolically inert patches of peptidoglycan. When combined with what we know about mutants affecting cellular morphology, these observations suggest that bacteria may fabricate specific shapes by directing the synthesis of two kinds of cell wall: a long‐lived, rigid framework that defines overall topology, and a metabolically plastic peptidoglycan whose shape is directed by internal scaffolds.
The COP9 signalosome is an essential regulator of development in the filamentous fungus Aspergillus nidulans
Authors: Busch Silke , Eckert Sabine E. , Krappmann Sven , Braus Gerhard H. 
Published: July 2003

SummaryThe COP9 signalosome (CSN) is a conserved multiprotein complex involved in regulation of eukaryotic development. The deduced amino acid sequences of two Aspergillus nidulans genes, csnD and csnE, show high identities to the fourth and fifth CSN subunits of higher eukaryotes. The csnD transcript is abundant during vegetative growth as well as development and the corresponding protein accumulates in the nucleus. Strains deleted for either csn gene are viable and show identical mutant phenotypes at conditions that allow development: hyphae appear partly red and contain cells of reduced size. Additionally, light dependence of propagation onset is affected. The Δcsn mutants are capable of initiating the sexual cycle and develop primordia, but maturation to sexual fruit bodies is blocked. This developmental arrest could not be overcome by overexpression of the sexual activator velvet (VEA). We conclude that the COP9 signalosome in A. nidulans is a key regulator of sexual development, and its proposed structural and functional conservation to the CSN of higher eukaryotes enables studies on this regulatory complex in a genetically amenable organism.
Low editing efficiency of GluR2 mRNA is associated with a low relative abundance of ADAR2 mRNA in white matter of normal human brain
Authors: Kawahara Yukio , Ito Kyoko , Sun Hui , Kanazawa Ichiro , Kwak Shin 
Published: July 2003

AbstractThe ionotropic glutamate receptor (GluR) subunits GluR2, GluR5 and GluR6 are subject to RNA editing at their Q/R sites, resulting in significant alterations in the channel properties of the receptors. RNA editing at the Q/R site of GluRs is both developmentally and regionally regulated. Here we provide the first quantitative measurements of both mRNAs of the GluR subunits and mRNAs of the RNA editing enzymes ADAR1–ADAR3 in a comparison of the efficiency of editing at the Q/R site with the expression levels of ADAR mRNA in human brain. We demonstrate that the Q/R site of GluRs in white matter is edited significantly less than in grey matter. In addition, by means of quantitative reverse transcription‐polymerase chain reaction methods, we demonstrate that the relative abundance of ADAR2 mRNA to GluR2 mRNA is significantly lower in white matter than in grey matter and that the GluR2 Q/R site editing decreased only when the ratio of ADAR2 mRNA (not that of ADAR1 mRNA) to GluR2 mRNA dropped below a threshold (20 × 10−3). These results suggest that Q/R site of GluRs editing is regulated in a regional, and hence presumably cell‐specific, manner and that the GluR2 Q/R site editing is critically regulated by ADAR2 in human brain.