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Search Results: 1 - 10 of 230609 matches for " John P. Hamilton "
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Current Demographics Suggest Future Energy Supplies Will Be Inadequate to Slow Human Population Growth
John P. DeLong,Oskar Burger,Marcus J. Hamilton
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0013206
Abstract: Influential demographic projections suggest that the global human population will stabilize at about 9–10 billion people by mid-century. These projections rest on two fundamental assumptions. The first is that the energy needed to fuel development and the associated decline in fertility will keep pace with energy demand far into the future. The second is that the demographic transition is irreversible such that once countries start down the path to lower fertility they cannot reverse to higher fertility. Both of these assumptions are problematic and may have an effect on population projections. Here we examine these assumptions explicitly. Specifically, given the theoretical and empirical relation between energy-use and population growth rates, we ask how the availability of energy is likely to affect population growth through 2050. Using a cross-country data set, we show that human population growth rates are negatively related to per-capita energy consumption, with zero growth occurring at ~13 kW, suggesting that the global human population will stop growing only if individuals have access to this amount of power. Further, we find that current projected future energy supply rates are far below the supply needed to fuel a global demographic transition to zero growth, suggesting that the predicted leveling-off of the global population by mid-century is unlikely to occur, in the absence of a transition to an alternative energy source. Direct consideration of the energetic constraints underlying the demographic transition results in a qualitatively different population projection than produced when the energetic constraints are ignored. We suggest that energetic constraints be incorporated into future population projections.
The New Catalogue of European Coleoptera
John Hamilton
Psyche , 1891, DOI: 10.1155/1891/63543
Abstract:
Electric Light Captures
John Hamilton
Psyche , 1889, DOI: 10.1155/1889/20196
Abstract:
An obstruction based approach to the Kochen-Specker theorem
John Hamilton
Mathematics , 1999, DOI: 10.1088/0305-4470/33/20/305
Abstract: In [1] it was shown that the Kochen Specker theorem can be written in terms of the non-existence of global elements of a certain varying set over the partially ordered set of boolean subalgebras of projection operators on some Hilbert space. In this paper, we show how obstructions to the construction of such global elements arise, and how this provides a new way of looking at proofs of the theorem.
mRNA-Seq Analysis of the Pseudoperonospora cubensis Transcriptome During Cucumber (Cucumis sativus L.) Infection
Elizabeth A. Savory, Bishwo N. Adhikari, John P. Hamilton, Brieanne Vaillancourt, C. Robin Buell, Brad Day
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0035796
Abstract: Pseudoperonospora cubensis, an oomycete, is the causal agent of cucurbit downy mildew, and is responsible for significant losses on cucurbit crops worldwide. While other oomycete plant pathogens have been extensively studied at the molecular level, Ps. cubensis and the molecular basis of its interaction with cucurbit hosts has not been well examined. Here, we present the first large-scale global gene expression analysis of Ps. cubensis infection of a susceptible Cucumis sativus cultivar, ‘Vlaspik’, and identification of genes with putative roles in infection, growth, and pathogenicity. Using high throughput whole transcriptome sequencing, we captured differential expression of 2383 Ps. cubensis genes in sporangia and at 1, 2, 3, 4, 6, and 8 days post-inoculation (dpi). Additionally, comparison of Ps. cubensis expression profiles with expression profiles from an infection time course of the oomycete pathogen Phytophthora infestans on Solanum tuberosum revealed similarities in expression patterns of 1,576–6,806 orthologous genes suggesting a substantial degree of overlap in molecular events in virulence between the biotrophic Ps. cubensis and the hemi-biotrophic P. infestans. Co-expression analyses identified distinct modules of Ps. cubensis genes that were representative of early, intermediate, and late infection stages. Collectively, these expression data have advanced our understanding of key molecular and genetic events in the virulence of Ps. cubensis and thus, provides a foundation for identifying mechanism(s) by which to engineer or effect resistance in the host.
Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis
Matthew A Campbell, Brian J Haas, John P Hamilton, Stephen M Mount, C Robin Buell
BMC Genomics , 2006, DOI: 10.1186/1471-2164-7-327
Abstract: A comprehensive analysis of alternative splicing was performed in rice that started with >1.1 million publicly available spliced ESTs and over 30,000 full length cDNAs in conjunction with the newly enhanced PASA software. A parallel analysis was performed with Arabidopsis to compare and ascertain potential differences between monocots and dicots. Alternative splicing is a widespread phenomenon (observed in greater than 30% of the loci with transcript support) and we have described nine alternative splicing variations. While alternative splicing has the potential to create many RNA isoforms from a single locus, the majority of loci generate only two or three isoforms and transcript support indicates that these isoforms are generally not rare events. For the alternate donor (AD) and acceptor (AA) classes, the distance between the splice sites for the majority of events was found to be less than 50 basepairs (bp). In both species, the most frequent distance between AA is 3 bp, consistent with reports in mammalian systems. Conversely, the most frequent distance between AD is 4 bp in both plant species, as previously observed in mouse. Most alternative splicing variations are localized to the protein coding sequence and are predicted to significantly alter the coding sequence.Alternative splicing is widespread in both rice and Arabidopsis and these species share many common features. Interestingly, alternative splicing may play a role beyond creating novel combinations of transcripts that expand the proteome. Many isoforms will presumably have negative consequences for protein structure and function, suggesting that their biological role involves post-transcriptional regulation of gene expression.Cultivated rice (Oryza sativa) is considered a model for species within the Poaceae family and, in particular, for agronomically important cereals such as maize (Zea mays), wheat (Triticum aestivum), and barley (Hordeum vulgare). Recently, map-based sequencing of a japonica subs
EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome
Fran?oise Thibaud-Nissen, Matthew Campbell, John P Hamilton, Wei Zhu, C Buell
BMC Genomics , 2007, DOI: 10.1186/1471-2164-8-388
Abstract: We have developed the Eukaryotic Community Annotation Package (EuCAP), an annotation tool, and have applied it to the rice genome. The primary level of curation by community annotators (CA) has been the annotation of gene families. Annotation can be submitted by email or through the EuCAP Web Tool. The CA models are aligned to the rice pseudomolecules and the coordinates of these alignments, along with functional annotation, are stored in the MySQL EuCAP Gene Model database. Web pages displaying the alignments of the CA models to the Osa1 Genome models are automatically generated from the EuCAP Gene Model database. The alignments are reviewed by the project annotators (PAs) in the context of experimental evidence. Upon approval by the PAs, the CA models, along with the corresponding functional annotations, are integrated into the Osa1 Genome Annotation. The CA annotations, grouped by family, are displayed on the Community Annotation pages of the project website http://rice.tigr.org webcite, as well as in the Community Annotation track of the Genome Browser.We have applied EuCAP to rice. As of July 2007, the structural and/or functional annotation of 1,094 genes representing 57 families have been deposited and integrated into the current gene set. All of the EuCAP components are open-source, thereby allowing the implementation of EuCAP for the annotation of other genomes. EuCAP is available at http://sourceforge.net/projects/eucap/ webcite.Accurate and consistent annotation of genomes presents a challenge that can be partially solved by automated and semi-automated annotation methods. Improvements in the structural annotation of gene models can be obtained through training of ab initio gene finders and, for eukaryotes, through empirical transcript support in the form of Expressed Sequence Tags (ESTs) and, more critically, full-length cDNAs [1-3]. In addition to structural annotation, in large-scale genome annotation projects functional annotation is performed in an a
Alternative Splicing of a Multi-Drug Transporter from Pseudoperonospora cubensis Generates an RXLR Effector Protein That Elicits a Rapid Cell Death
Elizabeth A. Savory, Cheng Zou, Bishwo N. Adhikari, John P. Hamilton, C. Robin Buell, Shin-Han Shiu, Brad Day
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0034701
Abstract: Pseudoperonospora cubensis, an obligate oomycete pathogen, is the causal agent of cucurbit downy mildew, a foliar disease of global economic importance. Similar to other oomycete plant pathogens, Ps. cubensis has a suite of RXLR and RXLR-like effector proteins, which likely function as virulence or avirulence determinants during the course of host infection. Using in silico analyses, we identified 271 candidate effector proteins within the Ps. cubensis genome with variable RXLR motifs. In extending this analysis, we present the functional characterization of one Ps. cubensis effector protein, RXLR protein 1 (PscRXLR1), and its closest Phytophthora infestans ortholog, PITG_17484, a member of the Drug/Metabolite Transporter (DMT) superfamily. To assess if such effector-non-effector pairs are common among oomycete plant pathogens, we examined the relationship(s) among putative ortholog pairs in Ps. cubensis and P. infestans. Of 271 predicted Ps. cubensis effector proteins, only 109 (41%) had a putative ortholog in P. infestans and evolutionary rate analysis of these orthologs shows that they are evolving significantly faster than most other genes. We found that PscRXLR1 was up-regulated during the early stages of infection of plants, and, moreover, that heterologous expression of PscRXLR1 in Nicotiana benthamiana elicits a rapid necrosis. More interestingly, we also demonstrate that PscRXLR1 arises as a product of alternative splicing, making this the first example of an alternative splicing event in plant pathogenic oomycetes transforming a non-effector gene to a functional effector protein. Taken together, these data suggest a role for PscRXLR1 in pathogenicity, and, in total, our data provide a basis for comparative analysis of candidate effector proteins and their non-effector orthologs as a means of understanding function and evolutionary history of pathogen effectors.
Expression Profiling of Cucumis sativus in Response to Infection by Pseudoperonospora cubensis
Bishwo N. Adhikari, Elizabeth A. Savory, Brieanne Vaillancourt, Kevin L. Childs, John P. Hamilton, Brad Day, C. Robin Buell
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0034954
Abstract: The oomycete pathogen, Pseudoperonospora cubensis, is the causal agent of downy mildew on cucurbits, and at present, no effective resistance to this pathogen is available in cultivated cucumber (Cucumis sativus). To better understand the host response to a virulent pathogen, we performed expression profiling throughout a time course of a compatible interaction using whole transcriptome sequencing. As described herein, we were able to detect the expression of 15,286 cucumber genes, of which 14,476 were expressed throughout the infection process from 1 day post-inoculation (dpi) to 8 dpi. A large number of genes, 1,612 to 3,286, were differentially expressed in pair-wise comparisons between time points. We observed the rapid induction of key defense related genes, including catalases, chitinases, lipoxygenases, peroxidases, and protease inhibitors within 1 dpi, suggesting detection of the pathogen by the host. Co-expression network analyses revealed transcriptional networks with distinct patterns of expression including down-regulation at 2 dpi of known defense response genes suggesting coordinated suppression of host responses by the pathogen. Comparative analyses of cucumber gene expression patterns with that of orthologous Arabidopsis thaliana genes following challenge with Hyaloperonospora arabidopsidis revealed correlated expression patterns of single copy orthologs suggesting that these two dicot hosts have similar transcriptional responses to related pathogens. In total, the work described herein presents an in-depth analysis of the interplay between host susceptibility and pathogen virulence in an agriculturally important pathosystem.
Analysis of four DLX homeobox genes in autistic probands
Steven P Hamilton, Jonathan M Woo, Elaine J Carlson, N?el Ghanem, Marc Ekker, John LR Rubenstein
BMC Genetics , 2005, DOI: 10.1186/1471-2156-6-52
Abstract: Sequencing of exons, exon/intron boundaries and known enhancers of DLX1, 2, 5 and 6 identified several nonsynonymous variants in DLX2 and DLX5 and a variant in a DLX5/6intragenic enhancer. The nonsynonymous variants were detected in 4 of 95 families from which samples were sequenced. Two of these four SNPs were not observed in 378 undiagnosed samples from North American populations, while the remaining 2 were seen in one sample each.Segregation of these variants in pedigrees did not generally support a contribution to autism susceptibility by these genes, although functional analyses may provide insight into the biological understanding of these important proteins.Autism is a severe heterogeneous neurobehavioral syndrome that becomes apparent in the first years of life [1-3] Autism is often viewed as a type of mental retardation, as most autistics have IQs lower than 70. However, autism is distinguished from other mental retardation syndromes by disproportionately severe deficits in language and social skills. Persons with some autistic features but with preserved language are often referred to as having Asperger's Syndrome [4].There has been much interest and work investigating the genetic basis of autism [5]. Twin studies have shown that autism is a strongly inherited disorder [2,6,7], as monozygotic twins are concordant for this syndrome substantially more frequently than are dizygotic twins. For reasons that are not yet understood, autism affects boys about four times more often than girls. Non-genetic etiological factors are under careful consideration [8], given the controversy over changing estimates of the incidence of autism over the past decades [9].Recently, we hypothesized that some forms of autism may be due to a disproportionate high level of excitation (or disproportionately weak inhibition) in neural circuits that mediate language and social behaviors [10]; related models have also been postulated [11,12]. A "noisy" (hyperexcitable, poorly functional
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