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Search Results: 1 - 10 of 155321 matches for " Andrew K. Benson "
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Drosophila melanogaster Selection for Survival of Bacillus cereus Infection: Life History Trait Indirect Responses
Junjie Ma,Andrew K. Benson,Stephen D. Kachman,Zhen Hu,Lawrence G. Harshman
International Journal of Evolutionary Biology , 2012, DOI: 10.1155/2012/935970
Abstract: To study evolved resistance/tolerance in an insect model, we carried out an experimental evolution study using D. melanogaster and the opportunistic pathogen B. cereus as the agent of selection. The selected lines evolved a 3.0- to 3.3-log increase in the concentration of spores required for 50% mortality after 18–24 generations of selection. In the absence of any treatment, selected lines evolved an increase in egg production and delayed development time. The latter response could be interpreted as a cost of evolution. Alternatively, delayed development might have been a target of selection resulting in increased adult fat body function including production of antimicrobial peptides, and, incidentally, yolk production for oocytes and eggs. When treated with autoclaved spores, the egg production difference between selected and control lines was abolished, and this response was consistent with the hypothesis of a cost of an induced immune response. Treatment with autoclaved spores also reduced life span in some cases and elicited early-age mortality in the selected and wound-control lines both of which were consistent with the hypothesis of a cost associated with induction of immune responses. In general, assays on egg production yielded key outcomes including the negative effect of autoclaved spores on egg production. 1. Introduction Genetic selection in the laboratory provides a powerful tool for evolutionary analysis of complex traits [1]. It has been used to study many phenomena at different levels of biological organization including life histories, physiology, demography and population dynamics, behavior, form, sex, whole-genome evolution, altruism, and speciation [2]. Selection results in amplification of genetic differences between selected and control lines which is the basis of phenotypic differentiation. Often, correlated (indirect) responses to selection are of particular interest in these experiments as they can suggest tradeoffs between traits. For example, selection for increased D. melanogaster life span and late-age reproduction resulted in decreased early-age reproduction [3, 4]. The nature of tradeoffs between traits is an important topic in life history evolution [5]. In the present study, the insect model D. melanogaster has been used in selection experiments for increased survival after bacterial infection. A previous study of responses in a laboratory selection experiment using Pseudomonas aeruginosa has examined the impact of D. melanogaster resistance on life history traits [6]. This study showed considerable costs in life span
Next-Generation Sequencing Reveals Significant Bacterial Diversity of Botrytized Wine
Nicholas A. Bokulich, C. M. Lucy Joseph, Greg Allen, Andrew K. Benson, David A. Mills
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0036357
Abstract: While wine fermentation has long been known to involve complex microbial communities, the composition and role of bacteria other than a select set of lactic acid bacteria (LAB) has often been assumed either negligible or detrimental. This study served as a pilot study for using barcoded amplicon next-generation sequencing to profile bacterial community structure in wines and grape musts, comparing the taxonomic depth achieved by sequencing two different domains of prokaryotic 16S rDNA (V4 and V5). This study was designed to serve two goals: 1) to empirically determine the most taxonomically informative 16S rDNA target region for barcoded amplicon sequencing of wine, comparing V4 and V5 domains of bacterial 16S rDNA to terminal restriction fragment length polymorphism (TRFLP) of LAB communities; and 2) to explore the bacterial communities of wine fermentation to better understand the biodiversity of wine at a depth previously unattainable using other techniques. Analysis of amplicons from the V4 and V5 provided similar views of the bacterial communities of botrytized wine fermentations, revealing a broad diversity of low-abundance taxa not traditionally associated with wine, as well as atypical LAB communities initially detected by TRFLP. The V4 domain was determined as the more suitable read for wine ecology studies, as it provided greater taxonomic depth for profiling LAB communities. In addition, targeted enrichment was used to isolate two species of Alphaproteobacteria from a finished fermentation. Significant differences in diversity between inoculated and uninoculated samples suggest that Saccharomyces inoculation exerts selective pressure on bacterial diversity in these fermentations, most notably suppressing abundance of acetic acid bacteria. These results determine the bacterial diversity of botrytized wines to be far higher than previously realized, providing further insight into the fermentation dynamics of these wines, and demonstrate the utility of next-generation sequencing for wine ecology studies.
A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences
David J Russell, Samuel F Way, Andrew K Benson, Khalid Sayood
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-601
Abstract: The performance of the proposed algorithm is validated via comparison to the popular DNA/RNA sequence clustering approach, CD-HIT-EST, and to the recently developed algorithm, UCLUST, using two different sets of 16S rDNA sequences from 2,255 genera. The proposed algorithm maintains a comparable CPU execution time with that of CD-HIT-EST which is much slower than UCLUST, and has successfully generated clusters with higher statistical accuracy than both CD-HIT-EST and UCLUST. The validation results are especially striking for large datasets.We introduce a fast and accurate clustering algorithm that relies on a grammar-based sequence distance. Its statistical clustering quality is validated by clustering large datasets containing 16S rDNA sequences.The amount of biological information being gathered is growing faster than the rate at which it can be analyzed. Data clustering, which compresses the problem space by reducing redundancy, is one viable tool for managing the explosive growth of data. In general, clustering algorithms are designed to operate on a large set of related values, eventually generating a smaller set of elements that represent groups of similar data points. A central data element may then be used as the sole representative of a group.Significant clustering work relating to bioinformatics may be traced to the late 1990 s when methods for quick generation of nonredundant (NR) protein databases were developed. These combined identical or nearly identical protein sequences into single entries [1-3]. The primary benefits of these methods include faster searches of the NR protein databases and reduced statistical bias in the query results [1]. Similarly, computer programs such as those in ICAtools [4] were developed for compressing DNA databases by removing redundant sequences found via clustering resulting in faster database queries. Note that the use of the term "clustering" in these applications differs from another use often found in the literature wh
Drosophila melanogaster Selection for Survival after Infection with Bacillus cereus Spores: Evolutionary Genetic and Phenotypic Investigations of Respiration and Movement
Junjie Ma,Andrew K. Benson,Stephen D. Kachman,Deidra J. Jacobsen
International Journal of Evolutionary Biology , 2013, DOI: 10.1155/2013/576452
Drosophila melanogaster Selection for Survival after Infection with Bacillus cereus Spores: Evolutionary Genetic and Phenotypic Investigations of Respiration and Movement
Junjie Ma,Andrew K. Benson,Stephen D. Kachman,Deidra J. Jacobsen,Lawrence G. Harshman
International Journal of Evolutionary Biology , 2013, DOI: 10.1155/2013/576452
Abstract: Laboratory populations of D. melanogaster have been subjected to selection for survival after live spores of B. cereus were introduced as a pathogenic agent. The present study was designed to investigate correlated traits: respiration as a metabolic trait and movement as a behavioral trait. An underlying hypothesis was that the evolution of increased survival after B. cereus infection exerts a metabolic cost associated with elevated immunity and this would be detected by increased respiration rates. There was support for this hypothesis in the male response to selection, but not for selected-line females. Two phenotypic effects were also observed in the study. Females especially showed a marked increase in respiration after mating compared to the other assay stages regardless of whether respiration was measured per fly or adjusted by lean mass or dry weight. Given that mating stimulates egg production, it is feasible that elevated metabolism was needed to provision oocytes with yolk. Females also moved less than males, perhaps due to behaviors related to oviposition whereas elevated male activity might be due to behaviors associated with seeking females and courtship. Relatively low movement of females indicated that their elevated respiration after mating was not due to a change in locomotion. 1. Introduction A tradeoff between immune function and reproduction has been observed in a range of studies. For example, an increase in reproductive effort is correlated with increased parasite incidence and disease [1, 2]. More generally, an increase in reproduction is associated with decreased immune system function [3, 4]. Two mechanisms have been proposed for this relationship. One is the Y model [5] in which there is an energetic competition between somatic function (immunity in the present study) and reproduction. The arms of the Y represent competition for energy between traits and the long axis represents resource input. Another potential mechanism for a tradeoff is a negative pleiotropic effect of hormones acting on two traits. An example is the effect of insulin signaling as a stimulator of reproduction and a suppressor of life span in D. melanogaster [6, 7]. In support of the role of hormones on insect life history tradeoffs, juvenile hormone (JH) has been shown to have negative pleiotropic effects on immunity and reproduction. In the flour beetle, Tenebrio molitor, mating causes a decrease in an immune system enzyme (phenoloxidase) by increasing the level of JH [8]. In the bee, Apis mellifera, a caste behavior was experimentally altered which
Genome evolution in major Escherichia coli O157:H7 lineages
Yongxiang Zhang, Chad Laing, Marina Steele, Kim Ziebell, Roger Johnson, Andrew K Benson, Eduardo Taboada, Victor PJ Gannon
BMC Genomics , 2007, DOI: 10.1186/1471-2164-8-121
Abstract: A total of 4,084 out of 6,057 ORFs were detected in all E. coli O157:H7 strains and 1,751 were variably present or absent. Based on this data, E. coli O157:H7 strains were divided into three distinct clusters, which consisted of 15 lineage I (LSPA type 111111), four lineage I/II (designated in this study) (LSPA type 211111) and 12 lineage II strains (LSPA 222222, 222211, 222212, and 222221), respectively. Eleven different genomic regions that were dominant in lineage I strains (present in ≥80% of lineage I and absent from ≥ 92% of lineage II strains) spanned segments containing as few as two and up to 25 ORFs each. These regions were identified within E. coli Sakai S-loops # 14, 16, 69, 72, 78, 83, 85, 153 and 286, Sakai phage 10 (S-loops # 91, 92 and 93) and a genomic backbone region. All four lineage I/II strains were of PT 2 and possessed eight of these 11 lineage I-dominant loci. Several differences in virulence-associated loci were noted between lineage I and lineage II strains, including divergence within S-loop 69, which encodes Shiga toxin 2, and absence of the non-LEE encoded effector genes nleF and nleH1-2 and the perC homologue gene pchD in lineage II strains.CGH data suggest the existence of two dominant lineages as well as LSPA type and PT-related subgroups within E. coli O157:H7. The genomic composition of these subgroups supports the phylogeny that has been inferred from other methods and further suggests that genomic divergence from an ancestral form and lateral gene transfer have contributed to their evolution. The genomic features identified in this study may contribute to apparent differences in the epidemiology and ecology of strains of different E. coli O157:H7 lineages.Enterohemorrhagic E. coli (EHEC) are associated with gastrointestinal and systemic illness in humans. This illness can range in severity from uncomplicated diarrhea to hemorrhagic colitis and the sometimes fatal hemolytic uremic syndrome [1-3]. EHEC strains possess a number of co
Galacticus: A Semi-Analytic Model of Galaxy Formation
Andrew J. Benson
Physics , 2010, DOI: 10.1016/j.newast.2011.07.004
Abstract: We describe a new, free and open source semi-analytic model of galaxy formation, Galacticus. The Galacticus model was designed to be highly modular to facilitate expansion and the exploration of alternative descriptions of key physical ingredients. We detail the Galacticus engine for evolving galaxies through a merging hierarchy of dark matter halos and give details of the specific implementations of physics currently available in Galacticus. Finally, we show results from an example model that is in reasonably good agreement with several observational datasets. We use this model to explore numerical convergence and to demonstrate the types of information which can be extracted from Galacticus.
Galaxy Formation Theory
Andrew J. Benson
Physics , 2010, DOI: 10.1016/j.physrep.2010.06.001
Abstract: We review the current theory of how galaxies form within the cosmological framework provided by the cold dark matter paradigm for structure formation. Beginning with the pre-galactic evolution of baryonic material we describe the analytical and numerical understanding of how baryons condense into galaxies, what determines the structure of those galaxies and how internal and external processes (including star formation, merging, active galactic nuclei etc.) determine their gross properties and evolution. Throughout, we highlight successes and failings of current galaxy formation theory. We include a review of computational implementations of galaxy formation theory and assess their ability to provide reliable modelling of this complex phenomenon. We finish with a discussion of several "hot topics" in contemporary galaxy formation theory and assess future directions for this field.
Measuring the Distribution of Galaxies Between Halos
Andrew J. Benson
Physics , 2001, DOI: 10.1046/j.1365-8711.2001.04470.x
Abstract: We develop a method to measure the probability, P(N;M), of finding N galaxies in a dark-matter halo of mass M from the theoretically determined clustering properties of dark-matter halos and the observationally measured clustering properties of galaxies. Knowledge of this function and the distribution of the dark matter completely specifies all clustering properties of galaxies on scales larger than the size of dark-matter halos. Furthermore, P(N;M) provides strong constraints on models of galaxy formation, since it depends upon the merger history of dark-matter halos and the galaxy-galaxy merger rate within halos. We show that measurements from a combination of the 2MASS and SDSS or 2dFGRS datasets will allow P(N;M) averaged over halos occupied by bright galaxies to be accurately measured for N=0-2.
The Origin of the Hubble Sequence in Lambda-CDM Cosmology
Andrew J. Benson,Nick Devereux
Physics , 2009, DOI: 10.1111/j.1365-2966.2009.16089.x
Abstract: The Galform semi-analytic model of galaxy formation is used to explore the mechanisms primarily responsible for the three types of galaxies seen in the local universe: bulge, bulge+disk and disk, identified with the visual morphological types E, S0/a-Sbc, and Sc-Scd, respectively. With a suitable choice of parameters the Galform model can accurately reproduce the observed local K_s-band luminosity function (LF) for galaxies split by visual morphological type. The successful set of model parameters is used to populate the Millennium Simulation with 9.4 million galaxies and their dark matter halos. The resulting catalogue is then used to explore the evolution of galaxies through cosmic history. The model predictions concur with recent observational results including the galaxy merger rate, the star formation rate and the seemingly anti-hierarchical evolution of ellipticals. However, the model also predicts significant evolution of the elliptical galaxy LF that is not observed. The discrepancy raises the possibility that samples of z~1 galaxies which have been selected using colour and morphological criteria may be contaminated with galaxies that are not actually ellipticals.
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