bluuebunny/crossref_metadata_2025_split huggingface dataset:
Moving on from Metabolic Scaling Theory: hierarchical models of tree growth and asymmetric competition for light
Authors: Coomes David A. , Lines Emily R. , Allen Robert B. 
Published: February 2011

Summary1. Coomes & Allen (2009)showed that the Metabolic Scaling Theory of Plant Growth (MST‐PG) has no empirical support, because the only piece of confirmatory evidence was an analysis of a small and noisy data set from which it was impossible to draw strong inferences. Our re‐analyses showed that MST‐PG predictions were contained within very broad 95% confidence intervals, creating an illusion of close adherence to theoretical predictions. In a response to our paper,Stark, Bentley & Enquist (2010)acknowledge these shortcomings.2.  We reasoned that MST‐PG makes inaccurate predictions because asymmetric competition for light is not included in the theoretical model. We argued that asymmetric competition has its greatest impact on small trees within populations, such that the mean size‐scaling relationship of the population has a greater exponent than that of trees growing without competitors (i.e. the slope predicted by MST‐PG).Stark, Bentley & Enquist (2010)appear to dispute this logic and criticize the statistical approach we developed to test our hypothesis.3.  Here we use Bayesian hierarchical models (BHMs) to re‐examine three forest data sets, and find no support for MST‐PG. Based on a large data set from New Zealand, the majority of tall tree species have scaling exponents greater than predicted by MST‐PG, suggesting that asymmetric competition may have influenced the scaling relationships. Parameters for many small tree and shrub species were very poorly estimated, in part because their size ranges were narrow, so these species cannot be used to argue for, or against, MST‐PG.4.  We hypothesize that scaling relationships are most affected by asymmetric competition in high‐productivity forests because, as many ecologists argue, competition for light is intense in such forests (the productivity‐dependent scaling hypothesis). We estimate growth scaling exponents forNothofagusforest sites which differed in above‐ground biomass (AGB) production. As predicted, scaling exponents were greater in sites with high AGB production and close to MST‐PG predictions in sites with low AGB production.5. Synthesis.Competition from taller neighbours has strong effects on tree growth, particularly in forests growing in productive locations. We continue to advocate for the inclusion of asymmetric competition into general models of tree growth, mortality, recruitment and size structure.
Understanding belief using citation networks
Authors: Greenberg Steven A. 
Published: February 2011

AbstractCitation is a powerful method for establishing belief. Published statements gain credibility when followed by citations. Citation in its purest form consists of the scholarly connection of authors' ideas and claims to existing literature, yet there are also non‐scholarly uses of citation that are best called citation distortions. Unfounded biomedical belief systems arising from citation distortions may become widely accepted as fact. The development of methodology for the study of citation distortions and belief systems regarding scientific claims was recently described. Here, I discuss further the methodological approaches to studying published scientific belief systems and identifying citation distortions.
Enhanced AFLP genome scans detect local adaptation in high‐altitude populations of a small rodent (Microtus arvalis)
Authors: FISCHER MARTIN C. , FOLL MATTHIEU , EXCOFFIER LAURENT , HECKEL GERALD 
Published: February 2011

AbstractAdaptation to adverse environmental conditions such as high altitude requires physiological and/or morphological changes. Genome scans provide a means to identify the genetic basis of such adaptations without previous knowledge about the particular genetic variants or traits under selection. In this study, we scanned 3027 amplified fragment length polymorphisms (AFLP) in four populations of the common vole Microtus arvalis for loci associated with local adaptation and high altitude. We investigated voles from two populations at high elevation (∼2000 m a.s.l.) representing the upper limit of the altitudinal distribution of the species and two geographically close low‐altitude populations (<600 m a.s.l.). Statistical analysis incorporated a new Bayesian FST outlier approach specifically developed for AFLP markers, which considers the intensity of AFLP bands instead of mere presence/absence and allows to derive population‐based estimates of allele frequencies and FIS values. Computer simulations showed that this approach increases the statistical power of the detection of AFLP markers under selection almost to the power of single nucleotide polymorphism (SNP) data without compromising specificity. Our enhanced genome scan resulted in 20 prime candidate markers for positive selection, which show mostly extremely high allele frequency differences between the low‐ and high‐altitude populations. The comparison of global‐ and pairwise‐enhanced genome scans demonstrated further that very strong selective signatures may also be associated with single populations suggesting the importance of local adaptation in alpine populations of common voles.
The transcriptomic responses of the eastern oyster, Crassostrea virginica, to environmental conditions
Authors: CHAPMAN ROBERT W. , MANCIA ANNALAURA , BEAL MARION , VELOSO ARTUR , RATHBURN CHARLES , BLAIR ANNE , HOLLAND A. F. , WARR G. W. , DIDINATO GUY , SOKOLOVA INNA M. , WIRTH EDWARD F. , DUFFY EDWARD , SANGER DENISE 
Published: February 2011

AbstractUnderstanding the mechanisms by which organisms adapt to environmental conditions is a fundamental question for ecology and evolution. In this study, we evaluate changes in gene expression of a marine mollusc, the eastern oyster Crassostrea virginica, associated with the physico‐chemical conditions and the levels of metals and other contaminants in their environment. The results indicate that transcript signatures can effectively disentangle the complex interactive gene expression responses to the environment and are also capable of disentangling the complex dynamic effects of environmental factors on gene expression. In this context, the mapping of environment to gene and gene to environment is reciprocal and mutually reinforcing. In general, the response of transcripts to the environment is driven by major factors known to affect oyster physiology such as temperature, pH, salinity, and dissolved oxygen, with pollutant levels playing a relatively small role, at least within the range of concentrations found in the studied oyster habitats. Further, the two environmental factors that dominate these effects (temperature and pH) interact in a dynamic and nonlinear fashion to impact gene expression. Transcriptomic data obtained in our study provide insights into the mechanisms of physiological responses to temperature and pH in oysters that are consistent with the known effects of these factors on physiological functions of ectotherms and indicate important linkages between transcriptomics and physiological outcomes. Should these linkages hold in further studies and in other organisms, they may provide a novel integrated approach for assessing the impacts of climate change, ocean acidification and anthropogenic contaminants on aquatic organisms via relatively inexpensive microarray platforms.
Stored sperm differs from ejaculated sperm by proteome alterations associated with energy metabolism in the honeybeeApis mellifera
Authors: POLAND VERONICA , EUBEL HOLGER , KING MICHAELA , SOLHEIM CORY , HARVEY MILLAR A. , BAER BORIS 
Published: February 2011

AbstractSperm are exposed to substantially different environments during their life history, such as seminal fluid or the female sexual tract, but remarkably little information is currently available about whether and how much sperm composition and function alters in these different environments. Here, we used the honeybeeApis melliferaand quantified differences in the abundance and activity of sperm proteins sampled either from ejaculates or from the female’s sperm storage organ. We find that stored and ejaculated sperm contain the same set of proteins but that the abundance of specific proteins differed substantially between ejaculated and stored sperm. Most proteins with a significant change in abundance are related to sperm energy metabolism. Enzymatic assays performed for a subset of these proteins indicate that specific protein activities differ between stored and ejaculated sperm and are typically higher in ejaculated compared to stored sperm. We provide evidence that the cellular machinery of sperm is plastic and differs between sperm within the ejaculate and within the female’s storage organ. Future work will be required to test whether these changes are a consequence of active adaptation or sperm senescence and whether they alter sperm performance in different chemical environments or impact on the cost of sperm storage by the female. However, these changes can be expected to influence sperm performance and therefore determine sperm viability or sperm competitiveness for storage or egg fertilization.
Dispersal strategies, secondary range expansion and invasion genetics of the nonindigenous round goby, Neogobius melanostomus, in Great Lakes tributaries
Authors: BRONNENHUBER JENNIFER E. , DUFOUR BRAD A. , HIGGS DENNIS M. , HEATH DANIEL D. 
Published: February 2011

AbstractDispersal strategies are important mechanisms underlying the spatial distribution and colonizing ability of all mobile species. In the current study, we use highly polymorphic microsatellite markers to evaluate local dispersal and colonization dynamics of the round goby (Neogobius melanostomus), an aquatic invader expanding its range from lake to river environments in its introduced North American range. Genetic structure, genotype assignment and genetic diversity were compared among 1262 round gobies from 20 river and four lake sites in three Great Lakes tributaries. Our results indicate that a combination of short‐distance diffusion and long‐distance dispersal, collectively referred to as ‘stratified dispersal’, is facilitating river colonization. Colonization proceeded upstream yearly (approximately 500 m/year; 2005–2009) in one of two temporal replicates while genetic structure was temporally stable. Contiguous dispersal from the lake was observed in all three rivers with a substantial portion of river fish (7.3%) identified as migrants. Genotype assignment indicated a separate introduction occurred upstream of the invasion front in one river. Genetic diversity was similar and relatively high among lake and recently colonized river populations, indicating that founder effects are mitigated through a dual‐dispersal strategy. The remarkable success of round goby as an aquatic invader stresses the need for better diffusion models of secondary range expansion for presumably sessile invasive species.
Multiple essential roles for EzrA in cell division of Staphylococcus aureus
Authors: Steele Victoria R. , Bottomley Amy L. , Garcia‐Lara Jorge , Kasturiarachchi Jagath , Foster Simon J. 
Published: February 2011

SummaryIn Bacillus subtilis, EzrA is involved in preventing aberrant formation of FtsZ rings and has also been implicated in the localization cycle of Pbp1. We have identified the orthologue of EzrA in Staphylococcus aureus to be essential for growth and cell division in this organism. Phenotypic analyses following titration of EzrA levels in S. aureus have shown that the protein is required for peptidoglycan synthesis as well as for assembly of the divisome at the midcell and cytokinesis. Protein interaction studies revealed that EzrA forms a complex with both the cytoplasmic components of the division machinery and those with periplasmic domains, suggesting that EzrA may be a scaffold molecule permitting the assembly of the division complex and forming an interface between the cytoplasmic cytoskeletal element FtsZ and the peptidoglycan biosynthetic apparatus active in the periplasm.
Characterization of Botryosphaeriaceae from plantation‐grown Eucalyptus species in South China
Authors: Chen S. F. , Pavlic D. , Roux J. , Slippers B. , Xie Y. J. , Wingfield M. J. , Zhou X. D. 
Published: February 2011

The Botryosphaeriaceae is a species‐rich family that includes pathogens of a wide variety of trees, including Eucalyptus species. Symptoms typical of infection by the Botryosphaeriaceae have recently been observed in Eucalyptus plantations in South China. The aim of this study was to identify the Botryosphaeriaceae associated with these symptoms. Isolates were collected from branch cankers and senescent twigs of different Eucalyptus spp. All isolates resembling Botryosphaeriaceae were separated into groups based on conidial morphology. Initial identifications were made using PCR‐RFLP fingerprinting, by digesting the ITS region of the rDNA operon with the restriction enzymes CfoI and KspI. Furthermore, to distinguish isolates in the Neofusicoccum parvum/N. ribis complex, a locus (BotF15) previously shown to define these species, was amplified and restricted with CfoI. Selected isolates were then identified using comparisons of DNA sequence data for the ITS rDNA and translation elongation factor 1‐alpha (TEF‐1α) gene regions. Based on anamorph morphology and DNA sequence comparisons, five species were identified: Lasiodiplodia pseudotheobromae, L. theobromae, Neofusicoccum parvum, N. ribis sensu lato and one undescribed taxon, for which the name Fusicoccum fabicercianum sp. nov. is provided. Isolates of all species gave rise to lesions on the stems of an E. grandis clone in a glasshouse inoculation trial and on the stems of five Eucalyptus genotypes inoculated in the field, where L. pseudotheobromae and L. theobromae were most pathogenic. The five Eucalyptus genotypes differed in their susceptibility to the Botryosphaeriaceae species suggesting that breeding and selection offers opportunity for disease avoidance in the future.
Temporal association of potato tuber development with susceptibility to common scab and Streptomyces scabiei‐induced responses in the potato periderm
Authors: Khatri B. B. , Tegg R. S. , Brown P. H. , Wilson C. R. 
Published: February 2011

Using hydroponics and novel non‐destructive pot culture systems which enable inoculation at specific tuber development stages, the dynamics of common scab infection patterns in potato were studied in order to provide more precise identification of tuber physiological factors associated with susceptibility. At the whole‐tuber level, infection percentages were greatest when Streptomyces scabiei inoculation occurred early; at 2 weeks after tuberization (WAT) 68% of tubers became infected, contrasting with late inoculation (8 WAT), when only 4% infection occurred. The first‐formed internodes were most susceptible to infection, whilst later‐forming and slower‐expanding internodes were less susceptible. Detailed tuber physiological examination of internode 2 showed that pathogen‐induced changes, including increased phellem (periderm) thickness, cell layers and phellem suberization (key physiological features believed critical to S. scabiei infection) were promoted through S. scabiei inoculation. Sequential harvesting showed enhanced phellem suberization (28% greater than the control) within 7 days of pathogen exposure, while phellem thickness and layer responses were also initiated early in the infection process (10–14 days after pathogen exposure) and these responses were independent of symptom expression. Differences in cultivar response were observed, with greater phellem suberization observed 10 days after tuberization (DAT) in the common‐scab‐tolerant cv. Russet Burbank than in the susceptible cv. Desiree. Likewise, Russet Burbank had thicker and more numerous cell layers in the phellem (up to eight cell layers) during early tuber growth (20–30 DAT) than Desiree (up to six cell layers).
The threat of wild habitat to scab resistant apple cultivars
Authors: Lê Van A. , Durel C.E. , Le Cam B. , Caffier V. 
Published: February 2011

Evaluations of plant resistance to pathogens are rarely made using isolates from wild habitats, although the heterogeneity of such habitats may generate pathogen diversity which could be a source of new virulence in cultivated habitats. The aim of this study was to investigate whether scab resistance factors, identified and characterized in apples using isolates of Venturia inaequalis from a cultivated habitat, remained effective against isolates from a wild habitat. Three V. inaequalis core collections originating from the cultivated apple Malus × domestica and from two wild species, M. sieversii and M. sylvestris, were established to maximize pathogen diversity. For each core collection, 10 isolates were inoculated in mixtures onto 51 genotypes from an apple progeny segregating for two qualitative resistance genes and six quantitative resistance loci (QRL). On each apple genotype, isolates that contributed to the scab symptoms were identified within the mixture using microsatellite markers. The most frequently detected isolates were inoculated singly to compare their aggressiveness according to their host origin. The results showed that isolates from a wild habitat were able to infect the susceptible apple genotypes. However, these isolates were never more aggressive than isolates from the cultivated habitat on the resistance factors tested. It can therefore be concluded that the resistance factors used in this study, identified with V. inaequalis isolates from a cultivated habitat, remained effective against isolates from M. sylvestris and M. sieversii.
Treatment of Multi‐Drug‐Resistant Tuberculosis in Mice with DNA Vaccines Alone or in Combination with Chemotherapeutic Drugs
Authors: Liang Y. , Wu X. , Zhang J. , Yang Y. , Wang L. , Bai X. , Yu Q. , Li N. , Li Z. 
Published: February 2011

AbstractThe problems of tuberculosis (TB) and its drug resistances are very severe in China. New therapeutic agents or regimens to treat multi‐drug‐resistant tuberculosis (MDR‐TB) are urgently needed. We studied the effects of Ag85A DNA vaccine alone or in combination with rifampin (RFP) or pyrazinamide (PZA) for the treatment of MDR‐TB in mice. Ag85A DNA vaccine significantly increased the production of IFN‐γ, but lowered the production of IL‐4. Seventy female BALB/c mice infected with Mycobacterium tuberculosis clinical isolate HB361, which was resistant to RFP and isoniazid but sensitive to PZA, were treated with plasmid pVAX1, RFP, PZA, M. vaccae vaccine, Ag85A DNA, Ag85A DNA combined with RFP or PZA, respectively. Ag85A DNA vaccine alone or in combination with RFP or PZA reduced the pulmonary and splenic bacterial loads by 1.03–1.38 logs, respectively. Ag85A DNA combined with conventional chemotherapy for the treatment of MDR‐TB might result in cure of MDR‐TB in developing countries.
Stimulatory Lipids Accumulate in the Mouse Liver within 30 min of Contact Sensitization to Facilitate the Activation of Naïve iNKT Cells in a CD1d‐Dependent Fashion
Authors: Dey N. , Szczepanik M. , Lau K. , Majewska‐Szczepanik M. , Askenase P. W. 
Published: February 2011

AbstractNatural killer T cells with invariant αβ‐T cell receptors (TCRs) (iNKT cells) constitute a lipid‐responsive arm of the innate immune system that has been implicated in the regulation or promotion of various immune, infectious and neoplastic processes. Contact sensitivity (CS), also known as contact hypersensitivity or allergic contact dermatitis, is one such immune process that begins with topical sensitization to an allergen and culminates in a localized cutaneous inflammatory response after challenge with the same allergen. CS depends on events initiated early in sensitization by hepatic iNKT cells. We have shown previously that these iNKT cells release IL‐4 early after skin sensitization to activate B‐1 B cells to produce IgM antibodies that aid in local recruitment of the effector T cells. Here, we utilize adoptive transfer techniques in several strains of knockout mice to demonstrate that hepatic lipids isolated 30 min after sensitization are significantly more stimulatory to naïve hepatic iNKT cells than hepatic lipids isolated after sham sensitization. These stimulatory hepatic lipids specifically affect iNKT cells and not B‐1 B cells. The downstream CS response is abrogated with anti‐CD1d‐blocking antibodies, suggesting a critical role of CD1d in the activation of hepatic iNKT cells with these lipids. Hepatocytes may not be essential, as donor hepatic iNKT cells can reconstitute CS without migrating to the recipient mouse liver. Rather, CD1d‐expressing liver mononuclear cells are sufficient for activation of iNKT cells. In conclusion, stimulatory lipids accumulate in the liver soon after sensitization and facilitate iNKT cell activation in a CD1d‐dependent yet potentially hepatocyte‐independent manner.
Differential Regulation of Notch Ligands in Dendritic Cells upon Interaction with T Helper Cells
Authors: Sauma D. , Espejo P. , Ramirez A. , Fierro A. , Rosemblatt M. , Bono M. R. 
Published: February 2011

AbstractThe Notch signalling pathway has recently been linked to T helper 1 (Th1)/T helper 2 (Th2) cell polarization via a mechanism involving differential expression of Notch ligands, Delta‐like and Jagged, in antigen‐presenting cells. However, whether stimuli other than pathogen‐derived factors are involved in the regulation of Notch ligand expression in dendritic cells (DCs) remains unknown. Here, we address the effect of T helper cells (Th1 and Th2) on Delta‐like 4 and Jagged 2 expression in bone marrow–derived DCs. We demonstrate that both Th1 and Th2 cells induce Delta‐like 4 mRNA expression in DCs, in a process that is, in part, mediated by CD40 signalling. In contrast, only Th2 cells induce a significant increase in Jagged 2 mRNA levels in DCs. Additionally, we show that IL‐4, a hallmark Th2 cytokine, plays a role in Jagged 2 expression, as evidenced by the fact that cholera toxin, a Th2‐promoting stimulus, induces Jagged 2 mRNA expression in DCs only in the presence of IL‐4. Finally, we demonstrate that DCs also express Notch 1 and that this expression is downregulated by IL‐4. These data suggest that Notch ligands are differentially regulated in DCs: Delta‐like 4 is regulated by T helper cells and by pathogen‐derived Th1 stimuli, whereas Jagged 2 is regulated by Th2 cells and pathogen‐derived Th2‐promoting stimuli. Based on our results, we propose that the positive feedback loop that Th2 cells exert on T cell polarization may involve the induction of Jagged 2 expression in DCs.