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81.
82.
Michael B. Morrissey Maartje Liefting 《Evolution; international journal of organic evolution》2016,70(9):1944-1959
Analysis of reaction norms, the functions by which the phenotype produced by a given genotype depends on the environment, is critical to studying many aspects of phenotypic evolution. Different techniques are available for quantifying different aspects of reaction norm variation. We examine what biological inferences can be drawn from some of the more readily applicable analyses for studying reaction norms. We adopt a strongly biologically motivated view, but draw on statistical theory to highlight strengths and drawbacks of different techniques. In particular, consideration of some formal statistical theory leads to revision of some recently, and forcefully, advocated opinions on reaction norm analysis. We clarify what simple analysis of the slope between mean phenotype in two environments can tell us about reaction norms, explore the conditions under which polynomial regression can provide robust inferences about reaction norm shape, and explore how different existing approaches may be used to draw inferences about variation in reaction norm shape. We show how mixed model‐based approaches can provide more robust inferences than more commonly used multistep statistical approaches, and derive new metrics of the relative importance of variation in reaction norm intercepts, slopes, and curvatures. 相似文献
83.
Antimicrobial susceptibility monitoring of dermatological bacterial pathogens isolated from diseased dogs and cats across Europe (ComPath results) 下载免费PDF全文
C. Ludwig A. de Jong H. Moyaert F. El Garch R. Janes U. Klein I. Morrissey J. Thiry M. Youala 《Journal of applied microbiology》2016,121(5):1254-1267
84.
Improved Luciferase Tagging System for Listeria monocytogenes Allows Real-Time Monitoring In Vivo and In Vitro 下载免费PDF全文
Christian U. Riedel Ian R. Monk Pat G. Casey David Morrissey Gerald C. O'Sullivan Mark Tangney Colin Hill Cormac G. M. Gahan 《Applied microbiology》2007,73(9):3091-3094
An improved system for luciferase tagging Listeria monocytogenes was developed by constructing a highly active, constitutive promoter. This construct gave 100-fold-higher activity in broth than any native promoter tested and allowed for imaging of lux-tagged L. monocytogenes in food products, during murine infections, and in tumor targeting studies. 相似文献
85.
Eduardo N Taboada Joanne M MacKinnon Christian C Luebbert Victor PJ Gannon John HE Nash Kris Rahn 《BMC evolutionary biology》2008,8(1):229
Background
Multi-Locus Sequence Typing (MLST) has emerged as a leading molecular typing method owing to its high ability to discriminate among bacterial isolates, the relative ease with which data acquisition and analysis can be standardized, and the high portability of the resulting sequence data. While MLST has been successfully applied to the study of the population structure for a number of different bacterial species, it has also provided compelling evidence for high rates of recombination in some species. We have analyzed a set of Campylobacter jejuni strains using MLST and Comparative Genomic Hybridization (CGH) on a full-genome microarray in order to determine whether recombination and high levels of genomic mosaicism adversely affect the inference of strain relationships based on the analysis of a restricted number of genetic loci. 相似文献86.
Aslam SN Newman MA Erbs G Morrissey KL Chinchilla D Boller T Jensen TT De Castro C Ierano T Molinaro A Jackson RW Knight MR Cooper RM 《Current biology : CB》2008,18(14):1078-1083
Bacterial pathogens and symbionts must suppress or negate host innate immunity. However, pathogens release conserved oligomeric and polymeric molecules or MAMPs (Microbial Associated Molecular Patterns), which elicit host defenses [1], [2] and [3]. Extracellular polysaccharides (EPSs) are key virulence factors in plant and animal pathogenesis, but their precise function in establishing basic compatibility remains unclear [4], [5], [6] and [7]. Here, we show that EPSs suppress MAMP-induced signaling in plants through their polyanionic nature [4] and consequent ability to chelate divalent calcium ions [8]. In plants, Ca2+ ion influx to the cytosol from the apoplast (where bacteria multiply [4], [5] and [9]) is a prerequisite for activation of myriad defenses by MAMPs [10]. We show that EPSs from diverse plant and animal pathogens and symbionts bind calcium. EPS-defective mutants or pure MAMPs, such as the flagellin peptide flg22, elicit calcium influx, expression of host defense genes, and downstream resistance. Furthermore, EPSs, produced by wild-type strains or purified, suppress induced responses but do not block flg22-receptor binding in Arabidopsis cells. EPS production was confirmed in planta, and the amounts in bacterial biofilms greatly exceed those required for binding of apoplastic calcium. These data reveal a novel, fundamental role for bacterial EPS in disease establishment, encouraging novel control strategies. 相似文献
87.
Robert C. Morrissey Douglass F. Jacobs John R. Seifert John A. Kershaw 《Plant Ecology》2010,208(1):21-34
Multifactor ecological classification systems are being developed for many regions. An element of these systems not yet well
understood is how disturbances, clearcutting in this instance, may alter the vegetative component of the classification units
at the stand and landscape levels. We sampled 1,096 plots in 21–35 year old naturally regenerated clearcuts on the Hoosier
National Forest (HNF) in south-central Indiana, USA. We examined overstory species composition of clearcut plots in comparison
to reference plots (80+ years old), both within and among six Ecological Landtype Phases (ELTPs) of two ecological sections
using non-metric multidimensional scaling and non-metric multi-response permutation procedures. Clearcutting drastically changed
species composition in comparison to reference plots within ELTPs ranging from mixed oak-dominated ridges and slopes to bottomland,
cove hardwood communities; Quercus species on ridges and slopes were replaced by Liriodendron tulipifera L. and, to a lesser degree, Prunus serotina Ehrh. and Acer rubrum L., in ELTPs of both sections. Contrasts of overstory species composition of reference plots exhibited differences among
ELTPs, but clearcut plots showed mixed results and indicated very similar species composition across all ELTPs. Autogenic
factors are likely the main drivers of overstory composition of clearcut sites. Species composition of ELTPs will continue
to develop in response to autogenic and allogenic factors over time, and differences among ELTPs may emerge in later stages
of stand development as the effects of allogenic factors accumulate. It is expected that L. tulipifera, a long-lived species, will be a dominant species in terms of basal area and density of all ELTPs in mature stands. Classification
systems not designed to deal with changes related to disturbance and a failure to predict successional pathways after disturbance
may limit their usefulness as a management tool in terms of overstory vegetation. For ecological classification systems to
be fully effective, we must better understand the role of disturbance in ecosystem function at many different scales and integrate
that knowledge into our decision-making and planning regimes to establish realistic and attainable objectives at multiple
scales. 相似文献
88.
P.W. Baker J. Kennedy J. Morrissey F. O’Gara A.D.W. Dobson J.R. Marchesi 《Journal of applied microbiology》2010,108(5):1668-1675
Aims: The conversion of cheap cellulosic biomass to more easily fermentable sugars requires the use of costly cellulases. We have isolated a series of marine sponge‐derived fungi and screened these for cellulolytic activity to determine the potential of this unique environmental niche as a source of novel cellulase activities. Methods and Results: Fungi were isolated from the marine sponge Haliclona simulans. Phylogenetic analysis of these and other fungi previously isolated from H. simulans showed fungi from three phyla with very few duplicate species. Cellulase activities were determined using plate‐based assays using different media and sea water concentrations while extracellular cellulase activities were determined using 3,5‐dinitrosalicylic acid (DNSA)‐based assays. Total and specific cellulase activities were determined using a range of incubation temperatures and compared to those for the cellulase overproducing mutant Hypocrea jecorina QM9414. Several of the strains assayed produced total or relative endoglucanase activities that were higher than H. jecorina, particularly at lower reaction temperatures. Conclusions: Marine sponges harbour diverse fungal species and these fungi are a good source of endoglucanase activities. Analysis of the extracellular endoglucanase activities revealed that some of the marine‐derived fungi produced high endoglucanase activities that were especially active at lower temperatures. Significance and Impact of the Study: Marine‐derived fungi associated with coastal marine sponges are a novel source of highly active endoglucanases with significant activity at low temperatures and could be a source of novel cellulase activities. 相似文献
89.
Chad Laing Cody Buchanan Eduardo N Taboada Yongxiang Zhang Andrew Kropinski Andre Villegas James E Thomas Victor PJ Gannon 《BMC bioinformatics》2010,11(1):461
Background
The pan-genome of a bacterial species consists of a core and an accessory gene pool. The accessory genome is thought to be an important source of genetic variability in bacterial populations and is gained through lateral gene transfer, allowing subpopulations of bacteria to better adapt to specific niches. Low-cost and high-throughput sequencing platforms have created an exponential increase in genome sequence data and an opportunity to study the pan-genomes of many bacterial species. In this study, we describe a new online pan-genome sequence analysis program, Panseq. 相似文献90.
M. J. Janeiro D. W. Coltman M. Festa‐Bianchet F. Pelletier M. B. Morrissey 《Journal of evolutionary biology》2017,30(2):270-288
Integral projection models (IPMs) are extremely flexible tools for ecological and evolutionary inference. IPMs track the distribution of phenotype in populations through time, using functions describing phenotype‐dependent development, inheritance, survival and fecundity. For evolutionary inference, two important features of any model are the ability to (i) characterize relationships among traits (including values of the same traits across ages) within individuals, and (ii) characterize similarity between individuals and their descendants. In IPM analyses, the former depends on regressions of observed trait values at each age on values at the previous age (development functions), and the latter on regressions of offspring values at birth on parent values as adults (inheritance functions). We show analytically that development functions, characterized this way, will typically underestimate covariances of trait values across ages, due to compounding of regression to the mean across projection steps. Similarly, we show that inheritance, characterized this way, is inconsistent with a modern understanding of inheritance, and underestimates the degree to which relatives are phenotypically similar. Additionally, we show that the use of a constant biometric inheritance function, particularly with a constant intercept, is incompatible with evolution. Consequently, current implementations of IPMs will predict little or no phenotypic evolution, purely as artefacts of their construction. We present alternative approaches to constructing development and inheritance functions, based on a quantitative genetic approach, and show analytically and through an empirical example on a population of bighorn sheep how they can potentially recover patterns that are critical to evolutionary inference. 相似文献