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Search Results: 1 - 10 of 221800 matches for " Patrick L. Jones "
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Duality, thermodynamics, and the linear programming problem in constraint-based models of metabolism
Patrick B. Warren,Janette L. Jones
Quantitative Biology , 2007, DOI: 10.1103/PhysRevLett.99.108101
Abstract: It is shown that the dual to the linear programming problem that arises in constraint-based models of metabolism can be given a thermodynamic interpretation in which the shadow prices are chemical potential analogues, and the objective is to minimise free energy consumption given a free energy drain corresponding to growth. The interpretation is distinct from conventional non-equilibrium thermodynamics, although it does satisfy a minimum entropy production principle. It can be used to motivate extensions of constraint-based modelling, for example to microbial ecosystems.
Impact of Sulfidation of Silver Nanoparticles on Established P. aeruginosa Biofilm  [PDF]
Yaolin Fennell, Patrick Ymele-Leki, Temitope Azeezat Adegboye, Kimberly L. Jones
Journal of Biomaterials and Nanobiotechnology (JBNB) , 2017, DOI: 10.4236/jbnb.2017.81006
Abstract: Silver nanoparticles (Ag-NPs), one of the most common types of nanomaterials in medical fields and consumer products, are known to have antimicrobial effects; these materials also undergo a series of chemical and biological transformations in the environment. Although the pristine form of silver nanoparticles has been studied, less is known about the impacts of the transformed Ag-NPs on biological systems. This knowledge gap hinders the progress of effectively assessing the impacts of Ag-NPs on the environment and human health. In this study, we demonstrate that the most common form of transformed Ag-NPs, sulfidized silver nano-particles (Ag2S-NPs), show less damage on established Pseudomonas aeruginosa GFP (ATCC? 10145 GFP?) biofilm than the pristine form of the nanoparticle. At a dosage of 0.625 mg/L, the total biomass in the biofilm decreased 64% after being exposed to Ag-NPs and 44% after exposure to Ag2S-NPs. Live biofilms were also interrogated. We observed high reduction in live population for biofilm exposed to Ag-NPs and relatively low reduction by Ag2S-NPs at exposure concentrations higher than 0.625 mg/L. Compared with Ag-NPs, the lower solubility of Ag2S-NPs results in less Ag+ diffusion into established biofilms. Our results suggest that the sulfidation of Ag-NPs reduces their impacts on established biofilms, indicating that the transformed Ag-NPs may have less environmental or human health risks.
Attracting cycles in p-adic dynamics and height bounds for post-critically finite maps
Robert L. Benedetto,Patrick Ingram,Rafe Jones,Alon Levy
Mathematics , 2012, DOI: 10.1215/00127094-2804674
Abstract: A rational function of degree at least two with coefficients in an algebraically closed field is post-critically finite (PCF) if all of its critical points have finite forward orbit under iteration. We show that the collection of PCF rational functions is a set of bounded height in the moduli space of rational functions over the complex numbers, once the well-understood family known as flexible Lattes maps is excluded. As a consequence, there are only finitely many conjugacy classes of non-Lattes PCF rational maps of a given degree defined over any given number field. The key ingredient of the proof is a non-archimedean version of Fatou's classical result that every attracting cycle of a rational function over the complex numbers attracts a critical point.
Flux networks in metabolic graphs
Patrick B. Warren,Silvio M. Duarte Queiros,Janette L. Jones
Quantitative Biology , 2008, DOI: 10.1088/1478-3975/6/4/046006
Abstract: A metabolic model can be represented as bipartite graph comprising linked reaction and metabolite nodes. Here it is shown how a network of conserved fluxes can be assigned to the edges of such a graph by combining the reaction fluxes with a conserved metabolite property such as molecular weight. A similar flux network can be constructed by combining the primal and dual solutions to the linear programming problem that typically arises in constraint-based modelling. Such constructions may help with the visualisation of flux distributions in complex metabolic networks. The analysis also explains the strong correlation observed between metabolite shadow prices (the dual linear programming variables) and conserved metabolite properties. The methods were applied to recent metabolic models for Escherichia coli, Saccharomyces cerevisiae, and Methanosarcina barkeri. Detailed results are reported for E. coli; similar results were found for the other organisms.
Heteromeric Anopheline Odorant Receptors Exhibit Distinct Channel Properties
Gregory M. Pask,Patrick L. Jones,Michael Rützler,David C. Rinker,Laurence J. Zwiebel
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0028774
Abstract: Insect odorant receptors (ORs) function as odorant-gated ion channels consisting of a conventional, odorant-binding OR and the Orco coreceptor. While Orco can function as a homomeric ion channel, the role(s) of the conventional OR in heteromeric OR complexes has largely focused only on odorant recognition.
Distinct Olfactory Signaling Mechanisms in the Malaria Vector Mosquito Anopheles gambiae
Chao Liu,R. Jason Pitts,Jonathan D. Bohbot,Patrick L. Jones,Guirong Wang,Laurence J. Zwiebel
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.1000467
Abstract: Anopheles gambiae is the principal Afrotropical vector for human malaria, in which olfaction mediates a wide range of both adult and larval behaviors. Indeed, mosquitoes depend on the ability to respond to chemical cues for feeding, host preference, and mate location/selection. Building upon previous work that has characterized a large family of An. gambiae odorant receptors (AgORs), we now use behavioral analyses and gene silencing to examine directly the role of AgORs, as well as a newly identified family of candidate chemosensory genes, the An. gambiae variant ionotropic receptors (AgIRs), in the larval olfactory system. Our results validate previous studies that directly implicate specific AgORs in behavioral responses to DEET as well as other odorants and reveal the existence of at least two distinct olfactory signaling pathways that are active in An. gambiae. One system depends directly on AgORs; the other is AgOR-independent and requires the expression and activity of AgIRs. In addition to clarifying the mechanistic basis for olfaction in this system, these advances may ultimately enhance the development of vector control strategies, targeting olfactory pathways in mosquitoes to reduce the catastrophic effects of malaria and other mosquito-borne diseases.
Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding
R Pitts, David C Rinker, Patrick L Jones, Antonis Rokas, Laurence J Zwiebel
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-271
Abstract: We compared chemosensory tissue transcriptomes to whole body transcriptomes of each sex to identify chemosensory enhanced genes. In the six data sets analyzed, we detected expression of nearly all known chemosensory genes and found them to be highly enriched in both olfactory tissues of males and females. While the maxillary palps of both sexes demonstrated strict chemosensory gene expression overlap, we observed acute differences in sensory specialization between male and female antennae. The relatively high expression levels of chemosensory genes in the female antennae reveal its role as an organ predominately assigned to chemosensation. Remarkably, the expression of these genes was highly conserved in the male antennae, but at much lower relative levels. Alternatively, consistent with a role in mating, the male antennae displayed significant enhancement of genes involved in audition, while the female enhancement of these genes was observed, but to a lesser degree.These findings suggest that the chemoreceptive spectrum, as defined by gene expression profiles, is largely similar in female and male An. gambiae. However, assuming sensory receptor expression levels are correlated with sensitivity in each case, we posit that male and female antennae are perceptive to the same stimuli, but possess inverse receptive prioritizations and sensitivities. Here we have demonstrated the use of RNA-seq to characterize the sensory specializations of an important disease vector and grounded future studies investigating chemosensory processes.Insects rely heavily upon chemosensation, the ability to detect and react to environmental chemical cues, in virtually every aspect of their life cycle [1]. Chemosensation is critical to food source identification, predator avoidance, oviposition site selection, kin recognition, mate choice, and toxic compound avoidance. In insects, chemosensory neurons are contained within distinct tissues on many parts of the body, most conspicuously on the
Distinct Olfactory Signaling Mechanisms in the Malaria Vector Mosquito Anopheles gambiae
Chao Liu equal contributor,R. Jason Pitts equal contributor,Jonathan D. Bohbot,Patrick L. Jones,Guirong Wang,Laurence J. Zwiebel
PLOS Biology , 2010, DOI: 10.1371/journal.pbio.1000467
Abstract: Anopheles gambiae is the principal Afrotropical vector for human malaria, in which olfaction mediates a wide range of both adult and larval behaviors. Indeed, mosquitoes depend on the ability to respond to chemical cues for feeding, host preference, and mate location/selection. Building upon previous work that has characterized a large family of An. gambiae odorant receptors (AgORs), we now use behavioral analyses and gene silencing to examine directly the role of AgORs, as well as a newly identified family of candidate chemosensory genes, the An. gambiae variant ionotropic receptors (AgIRs), in the larval olfactory system. Our results validate previous studies that directly implicate specific AgORs in behavioral responses to DEET as well as other odorants and reveal the existence of at least two distinct olfactory signaling pathways that are active in An. gambiae. One system depends directly on AgORs; the other is AgOR-independent and requires the expression and activity of AgIRs. In addition to clarifying the mechanistic basis for olfaction in this system, these advances may ultimately enhance the development of vector control strategies, targeting olfactory pathways in mosquitoes to reduce the catastrophic effects of malaria and other mosquito-borne diseases.
Generating the Pfaffian closure with total Pfaffian functions
Gareth Jones,Patrick Speissegger
Journal of Logic and Analysis , 2012, DOI: 10.4115/jla.v4i0.140
Abstract:
A Phase II Trial of the Epothilone B Analog Ixabepilone (BMS-247550) in Patients with Metastatic Melanoma
Patrick A. Ott,Anne Hamilton,Amanda Jones,Naomi Haas,Tsiporah Shore,Sandra Liddell,Paul J. Christos,L. Austin Doyle,Michael Millward,Franco M. Muggia,Anna C. Pavlick
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0008714
Abstract: Ixabepilone (BMS-247550), an epothilone B analog, is a microtubule stabilizing agent which has shown activity in several different tumor types and preclinical models in melanoma. In an open label, one-arm, multi-center phase II trial the efficacy and toxicity of this epothilone was investigated in two different cohorts: chemotherapy-na?ve (previously untreated) and previously treated patients with metastatic melanoma.
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