bluuebunny/crossref_metadata_2025_split huggingface dataset:
Occupancy estimation and the closure assumption
Authors: Rota Christopher T. , Fletcher Jr Robert J. , Dorazio Robert M. , Betts Matthew G. 
Published: November 2009

Summary 1.  Recent advances in occupancy estimation that adjust for imperfect detection have provided substantial improvements over traditional approaches and are receiving considerable use in applied ecology. To estimate and adjust for detectability, occupancy modelling requires multiple surveys at a site and requires the assumption of ‘closure’ between surveys, i.e. no changes in occupancy between surveys. Violations of this assumption could bias parameter estimates; however, little work has assessed model sensitivity to violations of this assumption or how commonly such violations occur in nature. 2.  We apply a modelling procedure that can test for closure to two avian point‐count data sets in Montana and New Hampshire, USA, that exemplify time‐scales at which closure is often assumed. These data sets illustrate different sampling designs that allow testing for closure but are currently rarely employed in field investigations. Using a simulation study, we then evaluate the sensitivity of parameter estimates to changes in site occupancy and evaluate a power analysis developed for sampling designs that is aimed at limiting the likelihood of closure. 3.  Application of our approach to point‐count data indicates that habitats may frequently be open to changes in site occupancy at time‐scales typical of many occupancy investigations, with 71% and 100% of species investigated in Montana and New Hampshire respectively, showing violation of closure across time periods of 3 weeks and 8 days respectively. 4.  Simulations suggest that models assuming closure are sensitive to changes in occupancy. Power analyses further suggest that the modelling procedure we apply can effectively test for closure. 5.
Synthesis and applications. Our demonstration that sites may be open to changes in site occupancy over time‐scales typical of many occupancy investigations, combined with the sensitivity of models to violations of the closure assumption, highlights the importance of properly addressing the closure assumption in both sampling designs and analysis. Furthermore, inappropriately applying closed models could have negative consequences when monitoring rare or declining species for conservation and management decisions, because violations of closure typically lead to overestimates of the probability of occurrence.
The maximum age of Hawaiian terrestrial lineages: geological constraints from Kōko Seamount
Authors: Clague David A. , Braga Juan C. , Bassi Davide , Fullagar Paul D. , Renema Willem , Webster Jody M. 
Published: November 2009

AbstractAim  To determine if Kōko Seamount submerged below sea level before Kure Island and Pearl and Hermes Reef formed, resulting in a period in which there were no extant islands. A period with no islands would eliminate prior terrestrial and shallow marine biotas that could migrate from island to island and require a restart of colonization from distant shores to populate the younger islands of the Hawaiian volcanic chain.Location  Emperor Seamount Chain, north‐central Pacific Ocean.Methods  We estimate subsidence rates for Kōko Seamount using ages determined from fossil large foraminifera and Sr‐isotopes, and maximum depths using palaeodepth estimates based on coralline algae. These data are combined with palaeolatitude changes as the Pacific Plate moved northwards, sea level variations, and sea surface temperature variations at the seamount through time to reconstruct the time and causes of submergence.Results  Rounded carbonate clasts include three facies: zooxanthelate corals, bioclastic packstones to rudstones, and rhodolith floatstones. Two rudstones contain relatively deep‐water, coralline algal rhodoliths and large foraminifera indicative of Aquitanian (20.4–20 Ma) and Burdigalian (20–16 Ma) stages of the Early Miocene, consistent with Sr‐isotope ages of algae and one sample of large foraminifera. Corals grew on Kōko Seamount from c. 50 to 27.1 ± 0.4 Ma, the youngest Sr‐isotope age of a coral sample. These shallow, warm‐water coral reefs came under increasing stress as the volcano subsided at 0.012 ± 0.003 mm yr−1, and migrated northwards, and as global climate cooled. The summit submerged and shallow coral reef growth ceased before 29 Ma, probably around 33 Ma. The volcano continued its slow subsidence, and deep‐water carbonates accumulated until they too were unable to keep pace, dying out at c. 16 Ma.Main conclusions  The final submergence of the summit of Kōko Seamount by about 33 Ma confirms that biota on older Hawaiian–Emperor Islands could not have migrated from island to island along the entire chain to eventually colonize the present Hawaiian Islands. There was a period between at least 33 and 29 Ma in which no islands existed, and distant colonization had to repopulate the younger portion of the Hawaiian chain, which began to emerge between about 29 and 23 Ma.
The relation between intrapersonal and interpersonal staff behaviour towards clients with ID and challenging behaviour: a validation study of the Staff–Client Interactive Behaviour Inventory
Authors: Willems A. P. A. M. , Embregts P. J. C. M. , Stams G. J. J. M. , Moonen X. M. H. 
Published: November 2009

AbstractBackground  Interpersonal staff behaviour is one of the instigating factors associated with challenging behaviour in clients with intellectual disabilities (ID). There are several studies focusing on the influence of intrapersonal staff characteristics – such as beliefs, attributions and emotional reactions – on staff behaviour. Little is known, however, about interpersonal staff behaviour itself. This study describes the development and validation of the Staff–Client Interactive Behaviour Inventory (SCIBI), measuring both intrapersonal and interpersonal staff behaviour in response to challenging behaviour in clients with ID.Method  A total of 292 staff members, employed in residential and community services, completed the SCIBI for 34 clients with ID and challenging behaviour.Results  Confirmatory factor analysis of a seven‐factor model – with assertive control, hostile, friendly and support‐seeking interpersonal behaviour; proactive thinking; self‐reflection; and critical expressed emotion as reliable factors – showed an exact fit to the data, indicating construct validity and reliability of the SCIBI. A series of multilevel regression analyses showed higher age of the client to be negatively associated with assertive control. Job experience, level of education, type and sex of staff predicted interpersonal behaviour. Also, intrapersonal staff behaviour, including critical expressed emotion, proactive thinking and self‐reflection, predicted interpersonal behaviour.Conclusions  The SCIBI can be used to identify staff intrapersonal and interpersonal behaviour towards clients with ID and challenging behaviour. Results obtained with the SCIBI can provide new directions for individual client treatment plans and staff training programmes.
A strong genetic footprint of the re‐introduction history of Alpine ibex (Capra ibex ibex)
Authors: BIEBACH IRIS , KELLER LUKAS F. 
Published: November 2009

AbstractA population’s neutral genetic variation is a composite of its size, degree of isolation and demographic history. Bottlenecks and founder events increase genetic drift, leading to the loss of genetic variation and increased genetic differentiation among populations. Gene flow has the opposite effects. Thus, gene flow can override the genetic patterns caused by founder events. Using 37 microsatellite loci, we investigated the effects of serial bottlenecks on genetic variation and differentiation among 42 Alpine ibex populations in Switzerland with known re‐introduction histories. We detected a strong footprint of re‐introduction events on contemporary genetic structure, with re‐introduction history explaining a substantial part of the genetic differentiation among populations. As a result of the translocation of a considerable number of individuals from the sole formerly surviving population in northern Italy, most of the genetic variation of the ancestral population is now present in the combined re‐introduced Swiss populations. However, re‐introductions split up the genetic variation among populations, such that each contemporary Swiss population showed lower genetic variation than the ancestral population. As expected, serial bottlenecks had different effects on the expected heterozygosity (He) and standardized number of alleles (sNa). While loss of sNa was higher in the first bottlenecks than in subsequent ones, He declined to a similar degree with each bottleneck. Thus, genetic drift was detected with each bottleneck, even when no loss of sNa was observed. Overall, more than a hundred years after the beginning of this successful re‐introduction programme, re‐introduction history was the main determinant of today’s genetic structure.
The noncosmopolitanism paradigm of freshwater zooplankton: insights from the global phylogeography of the predatory cladoceran Polyphemus pediculus (Linnaeus, 1761) (Crustacea, Onychopoda)
Authors: XU S. , HEBERT P. D. N. , KOTOV A. A. , CRISTESCU M. E. 
Published: November 2009

AbstractA major question in our understanding of eukaryotic biodiversity is whether small bodied taxa have cosmopolitan distributions or consist of geographically localized cryptic taxa. Here, we explore the global phylogeography of the freshwater cladoceran Polyphemus pediculus (Linnaeus, 1761) (Crustacea, Onychopoda) using two mitochondrial genes, cytochrome c oxidase subunit I and 16s ribosomal RNA, and one nuclear marker, 18s ribosomal RNA. The results of neighbour‐joining and Bayesian phylogenetic analyses reveal an exceptionally pronounced genetic structure at both inter‐ and intra‐continental scales. The presence of well‐supported, deeply divergent phylogroups across the Holarctic suggests that P. pediculus represents an assemblage of at least nine, largely allopatric cryptic species. Interestingly, all phylogenetic analyses support the reciprocal paraphyly of Nearctic and Palaearctic clades. Bayesian inference of ancestral distributions suggests that P. pediculus originated in North America or East Asia and that European lineages of Polyphemus were established by subsequent intercontinental dispersal events from North America. Japan and the Russian Far East harbour exceptionally high levels of genetic diversity at both regional and local scales. In contrast, little genetic subdivision is apparent across the formerly glaciated regions of Europe and North America, areas that historical demographic analyses suggest that were recolonized just 5500–24 000 years ago.
Coalescent under the evolution of coadaptation
Authors: RYO TAKAHASI K. 
Published: November 2009

AbstractAdaptation to novel environments arises either from new beneficial mutations or by utilizing pre‐existing genetic variation. When standing variation is used as the source of new adaptation, fitness effects of alleles may be altered through an environmental change. Alternatively, changes in epistatic genetic backgrounds may convert formerly neutral mutations into beneficial alleles in the new genetic background. By extending the coalescent theory to describe the genealogical histories of two interacting loci, I here investigated the hitchhiking effect of epistatic selection on the amount and pattern of sequence diversity at the linked neutral regions. Assuming a specific form of epistasis between two new mutations that are independently neutral, but together form a coadapted haplotype, I demonstrate that the footprints of epistatic selection differ markedly between the interacting loci depending on the order and relative timing of the two mutational events, even though both mutations are equally essential for the formation of an adaptive gene combination. Our results imply that even when neutrality tests could detect just a single instance of adaptive substitution, there may, in fact, be numerous other hidden mutations that are left undetected, but still play indispensable roles in the evolution of a new adaptation. We expect that the integration of the coalescent framework into the general theory of polygenic inheritance would clarify the connection between factors driving phenotypic evolution and their consequences on underlying DNA sequence changes, which should further illuminate the evolutionary foundation of coadapted systems.
High levels of population subdivision in a morphologically conserved Mediterranean toad (Alytes cisternasii) result from recent, multiple refugia: evidence from mtDNA, microsatellites and nuclear genealogies
Authors: GONÇALVES H. , MARTÍNEZ‐SOLANO I. , PEREIRA R. J. , CARVALHO B. , GARCÍA‐PARÍS M. , FERRAND N. 
Published: November 2009

AbstractPleistocene glaciations often resulted in differentiation of taxa in southern European peninsulas, producing the high levels of endemism characteristic of these regions (e.g. the Iberian Peninsula). Despite their small ranges, endemic species often exhibit high levels of intraspecific differentiation as a result of a complex evolutionary history dominated by successive cycles of fragmentation, expansion and subsequent admixture of populations. Most evidence so far has come from the study of species with an Atlantic distribution in northwestern Iberia, and taxa restricted to Mediterranean‐type habitats remain poorly studied. The Iberian Midwife toad (Alytes cisternasii) is a morphologically conserved species endemic to southwestern and central Iberia and a typical inhabitant of Mediterranean habitats. Applying highly variable genetic markers from both mitochondrial and nuclear genomes to samples collected across the species’ range, we found evidence of high population subdivision within A. cisternasii. Mitochondrial haplotypes and microsatellites show geographically concordant patterns of genetic diversity, suggesting population fragmentation into several refugia during Pleistocene glaciations followed by subsequent events of geographical and demographic expansions with secondary contact. In addition, the absence of variation at the nuclear β‐fibint7 and Ppp3caint4 gene fragments suggests that populations of A. cisternasii have been recurrently affected by episodes of extinction and recolonization, and that documented patterns of population subdivision are the outcome of recent and multiple refugia. We discuss the evolutionary history of the species with particular interest in the increasing relevance of Mediterranean refugia for the survival of genetically differentiated populations during the Pleistocene glaciations as revealed by studies in co‐distributed taxa.
Linking genotypes to phenotypes and fitness: how mechanistic biology can inform molecular ecology
Authors: DALZIEL ANNE C. , ROGERS SEAN M. , SCHULTE PATRICIA M. 
Published: November 2009

AbstractThe accessibility of new genomic resources, high‐throughput molecular technologies and analytical approaches such as genome scans have made finding genes contributing to fitness variation in natural populations an increasingly feasible task. Once candidate genes are identified, we argue that it is necessary to take a mechanistic approach and work up through the levels of biological organization to fully understand the impacts of genetic variation at these candidate genes. We demonstrate how this approach provides testable hypotheses about the causal links among levels of biological organization, and assists in designing relevant experiments to test the effects of genetic variation on phenotype, whole‐organism performance capabilities and fitness. We review some of the research programs that have incorporated mechanistic approaches when examining naturally occurring genetic and phenotypic variation and use these examples to highlight the value of developing a comprehensive understanding of the relationship between genotype and fitness. We give suggestions to guide future research aimed at uncovering and understanding the genetic basis of adaptation and argue that further integration of mechanistic approaches will help molecular ecologists better understand the evolution of natural populations.
The role of absC, a novel regulatory gene for secondary metabolism, in zinc‐dependent antibiotic production in Streptomyces coelicolor A3(2)
Authors: Hesketh Andy , Kock Holger , Mootien Saraspadee , Bibb Mervyn 
Published: November 2009

SummaryThe availability of zinc was shown to have a marked influence on the biosynthesis of actinorhodin in Streptomyces coelicolor A3(2). Production of actinorhodin and undecylprodigiosin was abolished when a novel pleiotropic regulatory gene, absC, was deleted, but only when zinc concentrations were low. AbsC was shown to control expression of the gene cluster encoding production of coelibactin, an uncharacterized non‐ribosomally synthesized peptide with predicted siderophore‐like activity, and the observed defect in antibiotic production was found to result from elevated expression of this gene cluster. Promoter regions in the coelibactin cluster contain predicted binding motifs for the zinc‐responsive regulator Zur, and dual regulation of coelibactin expression by zur and absC was demonstrated using strains engineered to contain deletions in either or both of these genes. An AbsC binding site was identified in a divergent promoter region within the coelibactin biosynthetic gene cluster, adjacent to a putative Zur binding site. Repression of the coelibactin gene cluster by both AbsC and Zur appears to be required to maintain appropriate intracellular levels of zinc in S. coelicolor.
The germinal centre kinase Don3 triggers the dynamic rearrangement of higher‐order septin structures during cytokinesis in Ustilago maydis
Authors: Böhmer Christian , Ripp Caroline , Bölker Michael 
Published: November 2009

SummaryThe dimorphic phytopathogenic fungus Ustilago maydis grows in its haploid phase by budding. Cytokinesis and separation of daughter cells are accomplished by the consecutive formation of two distinct septa. Here, we show that both septation events involve the dynamic rearrangement of septin assemblies from hourglass‐shaped collars into ring‐like structures. Using a chemical genetic approach we demonstrate that the germinal centre kinase Don3 triggers this septin reorganization during secondary septum formation. Although chemical inhibition of an analogue‐sensitive version of Don3 prevented septation, a stable septin collar was assembled at the presumptive septation site. Interestingly, the essential light chain of type II myosin, Cdc4, was already associated with this septin collar. Release of Don3 kinase inhibition triggered immediate dispersal of septin filaments and concomitant incorporation of Cdc4 into a contractile actomyosin ring, which also contained the F‐BAR domain protein Cdc15. Inhibition of actin polymerization or deletion of the cdc15 gene, did not affect assembly of the initial collar consisting of septin and myosin light chain. However, reassembly of septin filaments into a ring‐like structure was prevented in the absence of either F‐actin or Cdc15, indicating that septin ring formation in U. maydis depends on a functional contractile actomyosin ring.
Photooxidative stress‐induced and abundant small RNAs in Rhodobacter sphaeroides
Authors: Berghoff Bork A. , Glaeser Jens , Sharma Cynthia M. , Vogel Jörg , Klug Gabriele 
Published: November 2009

SummaryExposure to oxygen and light generates photooxidative stress by the bacteriochlorophyll a mediated formation of singlet oxygen (1O2) in Rhodobacter sphaeroides. Our study reports the genome‐wide search for small RNAs (sRNAs) involved in the regulatory response to 1O2. By using 454 pyrosequencing and Northern blot analysis, we identified 20 sRNAs from R. sphaeroides aerobic cultures or following treatment with 1O2 or superoxide (O–2). One sRNA was specifically induced by 1O2 and its expression depends on the extracytoplasmic function sigma factor RpoE. Two sRNAs induced by 1O2 and O–2 were cotranscribed with upstream genes preceded by promoters with target sequences for the alternative sigma factors RpoHI and RpoHII. The most abundant sRNA was processed in the presence of 1O2 but not by O–2. From this and a second sRNA a conserved 3′‐segment accumulated from a larger precursor. Absence of the RNA chaperone Hfq changed the half‐lives, abundance and processing of 1O2‐affected sRNAs. Orthologues of three sRNA genes are present in different alpha‐proteobacteria, but the majority was unique to R. sphaeroides or Rhodobacterales species. Our discovery that abundant sRNAs are affected by 1O2 exposure extends the knowledge on the role of sRNAs and Hfq in the regulatory response to oxidative stress.
Competitive activation of the Escherichia coli argO gene coding for an arginine exporter by the transcriptional regulators Lrp and ArgP
Authors: Peeters Eveline , Nguyen Le Minh Phu , Foulquié‐Moreno Maria , Charlier Daniel 
Published: November 2009

Summary In vivo and in vitro analyses indicate that transcription of the argO gene coding for an arginine exporter is regulated by the global transcriptional regulator Lrp, an effect that went by unnoticed in previous genome‐scale screenings of the Lrp regulatory network in Escherichia coli. Lrp activates the argO promoter fourfold; exogenous leucine antagonizes, but does not completely eliminate this effect. Activation by Lrp interferes with the previously demonstrated activation of the argO promoter by ArgP. This interference results from the mutual inhibitory binding of the two activators to overlapping targets. As a consequence, each regulator acts more potently in the absence of the other. Dimeric Lrp binds cooperatively to at least three regularly spaced semi‐palindromic binding sites. Leucine reduces complex formation approximately twofold but concomitantly enhances the cooperativity of the binding. Footprinting data suggest a severe Lrp‐induced deformation of the argO control region. Combined, the effector modulated activation of argO transcription by ArgP and Lrp must ensure an adapted and fine‐tuned synthesis of the transporter in response to environmental conditions. The repertoire of bacterial transcription regulation mechanisms is vast, but the competitive activation of a single promoter by two activator proteins as described here appears to be rare.
The BosR regulatory protein of Borrelia burgdorferi interfaces with the RpoS regulatory pathway and modulates both the oxidative stress response and pathogenic properties of the Lyme disease spirochete
Authors: Hyde Jenny A. , Shaw Dana K. , Smith III Roger , Trzeciakowski Jerome P. , Skare Jon T. 
Published: November 2009

Summary Borrelia burgdorferi, the Lyme disease spirochete, adapts as it moves between the arthropod and mammalian hosts that it infects. We hypothesize that BosR serves as a global regulator in B. burgdorferi to modulate the oxidative stress response and adapt to mammalian hosts. To test this hypothesis, a bosR mutant in a low‐passage B. burgdorferi isolate was constructed. The resulting bosR::kanR strain was altered when grown microaerobically or anaerobically suggesting that BosR is required for optimal replication under both growth conditions. The absence of BosR increased the sensitivity of B. burgdorferi to hydrogen peroxide and reduced the synthesis of Cdr and NapA, proteins important for cellular redox balance and the oxidative stress response, respectively, suggesting an important role for BosR in borrelial oxidative homeostasis. For the bosR mutant, the production of RpoS was abrogated and resulted in the loss of OspC and DbpA, suggesting that BosR interfaces with the Rrp2–RpoN–RpoS regulatory cascade. Consistent with the linkage to RpoS, cells lacking bosR were non‐infectious in the mouse model of infection. These results indicate that BosR is required for resistance to oxidative stressors and provides a regulatory response that is necessary for B. burgdorferi pathogenesis.