Christopher Dixon - Academia.edu (original) (raw)

Papers by Christopher Dixon

Journal of Biological Chemistry, Oct 1, 2015

Background: Direct targets for plant NLR proteins in immune signaling are largely unknown. Result... more Background: Direct targets for plant NLR proteins in immune signaling are largely unknown. Results: The Rx1 NLR protein of potato binds and distorts DNA following pathogen perception, resulting in immune activation. Conclusion: DNA is a direct signaling target for a plant NLR immune receptor. Significance: Plant NLR receptors might regulate immune transcriptional responses by directly interacting with plant chromatin.

Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable plants to recognize and respon... more Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable plants to recognize and respond to pathogen attack. Previously, we demonstrated that the Rx1 NLR of potato is able to bind and bend DNA in vitro. DNA binding in situ requires its genuine activation following pathogen perception. However, it is unknown whether other NLR proteins are also able to bind DNA. Nor is it known how DNA binding relates to the ATPase activity intrinsic to NLR switch function required to immune activation. Here we investigate these issues using a recombinant protein corresponding to the N-terminal coiled-coil and nucleotide-binding domain regions of the I-2 NLR of tomato. Wild type I-2 protein bound nucleic acids with a preference of ssDNA ≈ dsDNA > ssRNA, which is distinct from Rx1. I-2 induced bending and melting of DNA. Notably, ATP enhanced DNA binding relative to ADP in the wild type protein, the null P-loop mutant K207R, and the autoactive mutant S233F. DNA binding was found to activate the intrinsic ATPase activity of I-2. Because DNA binding by I-2 was decreased in the presence of ADP when compared with ATP, a cyclic mechanism emerges; activated ATP-associated I-2 binds to DNA, which enhances ATP hydrolysis, releasing ADP-bound I-2 from the DNA. Thus DNA binding is a general property of at least a subset of NLR proteins, and NLR activation is directly linked to its activity at DNA.

Journal of Biological Chemistry, 2016

Peer-review status of attached le: eerEreviewed Citation for published item: penykD F nd hixonD g... more Peer-review status of attached le: eerEreviewed Citation for published item: penykD F nd hixonD gFrF nd uittensD FrF nd ownsendD FhF nd hrpiesD qFtF nd ¦ lssonD vFEyF nd kkenD pFvFF nd gnnD wFtF @PHITA 9he tomto nuleotideEinding leuineErih repet @xvA immune reeptor sEP ouples hxeEinding to nuleotideEinding domin nuleotide exhngeF9D tournl of iologil hemistryFD PWI @QAF ppF IIQUEIIRUF

Genome Biology and Evolution, 2010

Different protein secondary structure elements have different physicochemical properties and role... more Different protein secondary structure elements have different physicochemical properties and roles in the protein, which may determine their evolutionary flexibility. However, it is not clear to what extent protein structure affects the way Darwinian selection acts at the amino acid level. Using phylogeny-based likelihood tests for positive selection, we have examined the relationship between protein secondary structure and selection across six species of Drosophila. We find that amino acids that form disordered regions, such as random coils, are far more likely to be under positive selection than expected from their proportion in the proteins, and residues in helices and b-structures are subject to less positive selection than predicted. In addition, it appears that sites undergoing positive selection are more likely than expected to occur close to one another in the protein sequence. Finally, on a genome-wide scale, we have determined that positively selected sites are found more frequently toward the gene ends. Our results demonstrate that protein structures with a greater degree of organization and strong hydrophobicity, represented here as helices and b-structures, are less tolerant to molecular adaptation than disordered, hydrophilic regions, across a diverse set of proteins.

Veterinary Ophthalmology, Jul 6, 2023

IntroductionThe aims of lens removal surgery are to re‐establish or preserve both a clear visual ... more IntroductionThe aims of lens removal surgery are to re‐establish or preserve both a clear visual axis and emmetropic vision. Trans‐scleral intraocular lens (IOL) fixation has been described in cases where lens capsule instability precludes the insertion of a prosthetic intraocular lens into the lens capsule. Previous techniques have necessitated enlargement of the corneal incision to accommodate either a rigid polymethylmethacrylate IOL or an acrylic foldable IOL inserted using forceps. This paper reports the modification of an endocapsular IOL to be used as an injectable suture‐fixated IOL introduced through a 2.8 mm corneal incision.Materials and MethodsAll cases underwent lens extraction by phacoemulsification followed by removal of the unstable lens capsule. A PFI X4 IOL (Medicontur) was modified to create four open‐loop haptics. The IOL was injected into the anterior chamber, each haptic was captured in a loop of suture introduced ab externo, and the lens was sutured with four‐point fixation.ResultsThe results from 20 eyes in 17 dogs are reported. Over an average follow‐up time of 14.5 months, vision was retained in 16/20 eyes. Vision was lost in four eyes due to corneal ulceration and ocular hypertension (1/20), retinal detachment (2/20), and Progressive Retinal Atrophy (1/20).ConclusionsThe modified PFI X4 proved suitable for injection and scleral fixation through a 2.8 mm corneal incision, with a success rate comparable to previously published techniques.

Journal of Small Animal Practice, Nov 19, 2021

ObjectivesTo report the outcomes following the insertion of a rhexis‐fixated prosthetic intraocul... more ObjectivesTo report the outcomes following the insertion of a rhexis‐fixated prosthetic intraocular lens (IOL) in dogs undergoing lens removal.Materials and MethodsThe results are from 30 eyes of 28 dogs, undergoing lendectomy, in which the lens capsule could not accommodate a conventional prosthetic endo‐capsular IOL. The reported cases had sustained either spontaneous or traumatic lens capsule rupture, or accidental intra‐operative iatrogenic lens capsule disruption, or had required a planned, large, anterior or posterior continuous curvilinear capsulorhexis, all of which precluded insertion of a prosthetic IOL within the lens capsule. An acrylic IOL (XVET; Medicontur) was modified and positioned across the anterior and/or posterior capsulorhexes.ResultsOther than haptic luxation in three cases, no complications were seen that were directly attributable to the rhexis‐fixated lens. Over a follow‐up period from three to 76 months (mean 20.7 months) 26/30 eyes remained visual. Blindness developed in three eyes due to retinal detachment and one eye was enucleated due to regrowth of a ciliary body adenoma.Clinical SignificanceRhexis fixation provided an alternative method to implant a prosthetic IOL when the lens capsule was unable to accommodate a conventional endo‐capsular IOL.

International Journal of Environmental Research and Public Health, Dec 11, 2020

Digital food ordering platforms are used by millions across the world and provide easy access to ... more Digital food ordering platforms are used by millions across the world and provide easy access to takeaway fast-food that is broadly, though not exclusively, characterised as energy dense and nutrient poor. Outlets are routinely rated for hygiene, but not for their healthiness. Nutritional information is mandatory in prepackaged foods, with many companies voluntarily using traffic light labels to support making healthier choices. We wanted to identify a feasible universal method to objectively score takeaway fast-food outlets listed on Just Eat that could provide users with an accessible rating that can infer an outlet's 'healthiness'. Using a sample of takeaway outlets listed on Just Eat, we obtained four complete assessments by nutrition researchers of each outlet's healthiness to create a cumulative score that ranged from 4 to 12. We then identified and manually extracted nutritional attributes from each outlet's digital menu, e.g., number of vegetables that have the potential to be numerated. Using generalized linear modelling we identified which attributes were linear predictors of an outlet's healthiness assessment from nutritional researchers. The availability of water, salad, and the diversity of vegetables were positively associated with academic researchers' assessment of an outlet's healthiness, whereas the availability of chips, desserts, and multiple meal sizes were negatively associated. This study shows promise for the feasibility of an objective measure of healthiness that could be applied to all outlet listings on Just Eat and other digital food outlet aggregation platforms. However, further research is required to assess the metric's validity, its desirability and value to users, and ultimately its potential influence on food choice behaviour.

Ecology of Freshwater Fish, Jun 1, 2009

– Burbot Lota lota are of global conservation concern particularly near the southern extent of ... more – Burbot Lota lota are of global conservation concern particularly near the southern extent of the species range. Populations in small streams lack quantitative descriptions of resource selection. Microhabitat and reach‐scale habitat were surveyed at occupied and unoccupied locations. Data were analyzed with logistic regression to develop resource selection function models which predicted the probability of occurrence and abundance categories for microhabitat and reach‐scale habitat, respectively. Information‐theoretic model selection methods were used in an exploratory context, and four competing models were multi‐model averaged to create a microhabitat resource selection function. The sum of Akaike’s Information Criterion weights across the four competing models indicated that substrate type, substrate embeddedness, and depth were equally the most important microhabitat explanatory variables. At the reach scale, high correlation among explanatory variables precluded multivariate model development. Stream‐reach gradient was the most supported univariate model. Three additional models competed as important; mean summer temperature, sinuosity, and dominant substrate type. The created resource selection functions can be used in ranking potential translocation sites, used in instream flow assessments, and provide habitat selection information that can provide context for habitat management decisions.

Journal of Evolutionary Biology, Nov 2, 2010

Journal of Freshwater Ecology, Mar 1, 2010

We studied the population structure and diet of burbot (Lota lota) listed as stateendangered and ... more We studied the population structure and diet of burbot (Lota lota) listed as stateendangered and inhabiting small streams near the southern extent of the species' North American range. The size structure was truncated, with a mean total length of 191 mm and range of 84-356 mm. A subsample of individuals (n=32) were euthanized, and age estimates from otoliths revealed surprisingly short lifespans (maximum age of five years). An age-length key was then used to assign ages proportionately to the larger sample. and 80% were estimated to have been age 2 and age 3. Burbot stomach contents were removed with gastric lavage from 120 individuals during summer sampling that occurred at fourhour intervals for 24 h. Burbot specialized on Ephemeroptera, and consumed a variety of other invertebrate prey; surprisingly. fish were only found in three individuals. While similar to other reports of burbot in small streams, (e.g. small body sizes, earlier maturation, short-lifespan, invertebrate-centered diet) the population demographics were considerably different from 'typical' burbot populations occurring in lakes, large rivers, and reservoirs.

Transactions of The American Fisheries Society, Sep 1, 2011

We monitored survival and tag loss among Moapa White River springfish Crenichthys baileyi moapae ... more We monitored survival and tag loss among Moapa White River springfish Crenichthys baileyi moapae that were surgically implanted with passive integrated transponder (PIT; 9 × 2 mm) tags. The fish used in the study ranged from 40 to 67 mm in total length and from 1.0 to 6.5 g in mass; the PIT tag: body weight ratios were 1.0–6.1%. Fish were held for 41 d in live cages within a small, warm desert stream. Survival did not differ between untagged control fish (94.5%) and tagged fish (95.6%). Survival did not appear to be influenced by fish size or PIT tag: body weight ratio, but the small number of fish that died precluded a detailed analysis. Tag retention was 100% among the 86 fish that survived over the 41 d. Our results suggest that surgically implanting 9‐mm PIT tags into Moapa White River springfish as small as 40 mm is an effective method for marking them because it has minimal impacts on survival and tag retention is high. More work is needed on the effects of PIT tagging on growth and other performance metrics of springfish and other small desert fishes.

Journal of Biological Chemistry, Mar 1, 2018

Edited by Joseph M. Jez Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable the im... more Edited by Joseph M. Jez Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable the immune system to recognize and respond to pathogen attack. An early consequence of immune activation is transcriptional reprogramming, and some NLRs have been shown to act in the nucleus and interact with transcription factors. The Rx1 NLR protein of potato is further able to bind and distort double-stranded DNA. However, Rx1 host targets that support a role for Rx1 in transcriptional reprogramming at DNA are unknown. Here, we report a functional interaction between Rx1 and NbGlk1, a Golden2-like transcription factor. Rx1 binds to NbGlk1 in vitro and in planta. NbGlk1 binds to known Golden2like consensus DNA sequences. Rx1 reduces the binding affinity of NbGlk1 for DNA in vitro. NbGlk1 activates cellular responses to potato virus X, whereas Rx1 associates with NbGlk1 and prevents its assembly on DNA in planta unless activated by PVX. This study provides new mechanistic insight into how an NLR can coordinate an immune signaling response at DNA following pathogen perceptions.

Evolution, Jan 17, 2012

The mechanics of speciation with gene flow are still unclear. Disparity among genes in population... more The mechanics of speciation with gene flow are still unclear. Disparity among genes in population differentiation (F ST) between diverging species is often interpreted as evidence for semipermeable species boundaries, with selection preventing "key" genes from introgressing despite ongoing gene flow. However, F ST can remain high before it reaches equilibrium between the lineage sorting of species divergence and the homogenizing effects of gene flow (via secondary contact). Thus, when interpreting F ST , the dynamics of drift, gene flow, and selection need to be taken into account. We illustrate this view with a multigenic analyses of gene flow and selection in three closely related Silene species, S. latifolia, S. dioica, and S. diclinis. We report that although S. diclinis appears to have evolved in allopatry, isolation with (bidirectional) gene flow between S. latifolia and S. dioica is likely, perhaps as a result of parapatric speciation followed by more extensive sympatry. Interestingly, we detected the signatures of apparently independent instances of positive selection at the same locus in S. latifolia and S. dioica. Despite gene flow between the species, the adaptive alleles have not crossed the species boundary, suggesting that this gene has independently undergone species-specific (diversifying or parallel) selection.

The family Meliaceace contains some of the world's finest grade cabinet timbers. These includ... more The family Meliaceace contains some of the world's finest grade cabinet timbers. These include the Honduran mahogany (Swietenia macrophylla), West Indian mahogany (S. mahogani), Ugandan mahogany (Entandrophragma sp.), Asian Chukrasia (Chukrasia tabularis) and the Australian red cedar or Indian Toon (T. ciliata). Timber of T. ciliata was exported from Australia to Calcutta, India, in 1795 just seven years after the first British settlement was established in Sydney, thus becoming Australia's first export. The harvesting of this species was very important to the economy of the early European settlement and the timber getters helped open up the coastal forests for later agricultural activities (Boland, 1997). The species was also arguably the first Australian plant species to have conservation measures placed upon it (Boland, 1997) when it was realised that the species was rapidly disappearing in areas near Sydney. In India, thirty years ago, timber of T. ciliata was said to be...

International Journal of Environmental Research and Public Health, 2020

Digital food ordering platforms are used by millions across the world and provide easy access to ... more Digital food ordering platforms are used by millions across the world and provide easy access to takeaway fast-food that is broadly, though not exclusively, characterised as energy dense and nutrient poor. Outlets are routinely rated for hygiene, but not for their healthiness. Nutritional information is mandatory in pre-packaged foods, with many companies voluntarily using traffic light labels to support making healthier choices. We wanted to identify a feasible universal method to objectively score takeaway fast-food outlets listed on Just Eat that could provide users with an accessible rating that can infer an outlet’s ‘healthiness’. Using a sample of takeaway outlets listed on Just Eat, we obtained four complete assessments by nutrition researchers of each outlet’s healthiness to create a cumulative score that ranged from 4 to 12. We then identified and manually extracted nutritional attributes from each outlet’s digital menu, e.g., number of vegetables that have the potential to...

Proceedings of the Annual Conference of CAIS / Actes du congrès annuel de l'ACSI, 2013

While the dramatic growth of book superstores has been of great concern to public libraries, ther... more While the dramatic growth of book superstores has been of great concern to public libraries, there has been little serious research about what people actually do in bookstores. How much are their behaviours like those that typically occur in libraries? To what extent are they different? To answer these questions an unobtrusive observational study is underway at three Chapters bookstores in two large Ontario cities.

Proceedings of the Annual Conference of CAIS / Actes du congrès annuel de l'ACSI, 2013

Unobtrusive observation in nine sites in two public libraries in Southern Ontario explored user c... more Unobtrusive observation in nine sites in two public libraries in Southern Ontario explored user compliance with posted rules of conduct. With the exception of children who were frequently loud and rambunctious, most users followed the rules. This finding is consistent with Goffman’s idea that behaviour in public places is governed by normative assumptions of public order.L’observation non obstructive effectuée dans neuf sites de deux bibliothèques publiques du sud de l’Ontario a examiné la conformité de l’utilisateur avec les règles de conduite affichées. À l’exception des enfants qui étaient fréquemment bruyants et querelleurs, la plupart des utilisateurs ont suivi le règlement. Ces résultats sont conformes avec l’idée de Goffman affirmant que le comportement dans les endroits publics est régi par des conventions normatives au sujet de l’ordre public.

Journal of Biological Chemistry, Oct 1, 2015

Background: Direct targets for plant NLR proteins in immune signaling are largely unknown. Result... more Background: Direct targets for plant NLR proteins in immune signaling are largely unknown. Results: The Rx1 NLR protein of potato binds and distorts DNA following pathogen perception, resulting in immune activation. Conclusion: DNA is a direct signaling target for a plant NLR immune receptor. Significance: Plant NLR receptors might regulate immune transcriptional responses by directly interacting with plant chromatin.

Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable plants to recognize and respon... more Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable plants to recognize and respond to pathogen attack. Previously, we demonstrated that the Rx1 NLR of potato is able to bind and bend DNA in vitro. DNA binding in situ requires its genuine activation following pathogen perception. However, it is unknown whether other NLR proteins are also able to bind DNA. Nor is it known how DNA binding relates to the ATPase activity intrinsic to NLR switch function required to immune activation. Here we investigate these issues using a recombinant protein corresponding to the N-terminal coiled-coil and nucleotide-binding domain regions of the I-2 NLR of tomato. Wild type I-2 protein bound nucleic acids with a preference of ssDNA ≈ dsDNA > ssRNA, which is distinct from Rx1. I-2 induced bending and melting of DNA. Notably, ATP enhanced DNA binding relative to ADP in the wild type protein, the null P-loop mutant K207R, and the autoactive mutant S233F. DNA binding was found to activate the intrinsic ATPase activity of I-2. Because DNA binding by I-2 was decreased in the presence of ADP when compared with ATP, a cyclic mechanism emerges; activated ATP-associated I-2 binds to DNA, which enhances ATP hydrolysis, releasing ADP-bound I-2 from the DNA. Thus DNA binding is a general property of at least a subset of NLR proteins, and NLR activation is directly linked to its activity at DNA.

Journal of Biological Chemistry, 2016

Peer-review status of attached le: eerEreviewed Citation for published item: penykD F nd hixonD g... more Peer-review status of attached le: eerEreviewed Citation for published item: penykD F nd hixonD gFrF nd uittensD FrF nd ownsendD FhF nd hrpiesD qFtF nd ¦ lssonD vFEyF nd kkenD pFvFF nd gnnD wFtF @PHITA 9he tomto nuleotideEinding leuineErih repet @xvA immune reeptor sEP ouples hxeEinding to nuleotideEinding domin nuleotide exhngeF9D tournl of iologil hemistryFD PWI @QAF ppF IIQUEIIRUF

Genome Biology and Evolution, 2010

Different protein secondary structure elements have different physicochemical properties and role... more Different protein secondary structure elements have different physicochemical properties and roles in the protein, which may determine their evolutionary flexibility. However, it is not clear to what extent protein structure affects the way Darwinian selection acts at the amino acid level. Using phylogeny-based likelihood tests for positive selection, we have examined the relationship between protein secondary structure and selection across six species of Drosophila. We find that amino acids that form disordered regions, such as random coils, are far more likely to be under positive selection than expected from their proportion in the proteins, and residues in helices and b-structures are subject to less positive selection than predicted. In addition, it appears that sites undergoing positive selection are more likely than expected to occur close to one another in the protein sequence. Finally, on a genome-wide scale, we have determined that positively selected sites are found more frequently toward the gene ends. Our results demonstrate that protein structures with a greater degree of organization and strong hydrophobicity, represented here as helices and b-structures, are less tolerant to molecular adaptation than disordered, hydrophilic regions, across a diverse set of proteins.

Veterinary Ophthalmology, Jul 6, 2023

IntroductionThe aims of lens removal surgery are to re‐establish or preserve both a clear visual ... more IntroductionThe aims of lens removal surgery are to re‐establish or preserve both a clear visual axis and emmetropic vision. Trans‐scleral intraocular lens (IOL) fixation has been described in cases where lens capsule instability precludes the insertion of a prosthetic intraocular lens into the lens capsule. Previous techniques have necessitated enlargement of the corneal incision to accommodate either a rigid polymethylmethacrylate IOL or an acrylic foldable IOL inserted using forceps. This paper reports the modification of an endocapsular IOL to be used as an injectable suture‐fixated IOL introduced through a 2.8 mm corneal incision.Materials and MethodsAll cases underwent lens extraction by phacoemulsification followed by removal of the unstable lens capsule. A PFI X4 IOL (Medicontur) was modified to create four open‐loop haptics. The IOL was injected into the anterior chamber, each haptic was captured in a loop of suture introduced ab externo, and the lens was sutured with four‐point fixation.ResultsThe results from 20 eyes in 17 dogs are reported. Over an average follow‐up time of 14.5 months, vision was retained in 16/20 eyes. Vision was lost in four eyes due to corneal ulceration and ocular hypertension (1/20), retinal detachment (2/20), and Progressive Retinal Atrophy (1/20).ConclusionsThe modified PFI X4 proved suitable for injection and scleral fixation through a 2.8 mm corneal incision, with a success rate comparable to previously published techniques.

Journal of Small Animal Practice, Nov 19, 2021

ObjectivesTo report the outcomes following the insertion of a rhexis‐fixated prosthetic intraocul... more ObjectivesTo report the outcomes following the insertion of a rhexis‐fixated prosthetic intraocular lens (IOL) in dogs undergoing lens removal.Materials and MethodsThe results are from 30 eyes of 28 dogs, undergoing lendectomy, in which the lens capsule could not accommodate a conventional prosthetic endo‐capsular IOL. The reported cases had sustained either spontaneous or traumatic lens capsule rupture, or accidental intra‐operative iatrogenic lens capsule disruption, or had required a planned, large, anterior or posterior continuous curvilinear capsulorhexis, all of which precluded insertion of a prosthetic IOL within the lens capsule. An acrylic IOL (XVET; Medicontur) was modified and positioned across the anterior and/or posterior capsulorhexes.ResultsOther than haptic luxation in three cases, no complications were seen that were directly attributable to the rhexis‐fixated lens. Over a follow‐up period from three to 76 months (mean 20.7 months) 26/30 eyes remained visual. Blindness developed in three eyes due to retinal detachment and one eye was enucleated due to regrowth of a ciliary body adenoma.Clinical SignificanceRhexis fixation provided an alternative method to implant a prosthetic IOL when the lens capsule was unable to accommodate a conventional endo‐capsular IOL.

International Journal of Environmental Research and Public Health, Dec 11, 2020

Digital food ordering platforms are used by millions across the world and provide easy access to ... more Digital food ordering platforms are used by millions across the world and provide easy access to takeaway fast-food that is broadly, though not exclusively, characterised as energy dense and nutrient poor. Outlets are routinely rated for hygiene, but not for their healthiness. Nutritional information is mandatory in prepackaged foods, with many companies voluntarily using traffic light labels to support making healthier choices. We wanted to identify a feasible universal method to objectively score takeaway fast-food outlets listed on Just Eat that could provide users with an accessible rating that can infer an outlet's 'healthiness'. Using a sample of takeaway outlets listed on Just Eat, we obtained four complete assessments by nutrition researchers of each outlet's healthiness to create a cumulative score that ranged from 4 to 12. We then identified and manually extracted nutritional attributes from each outlet's digital menu, e.g., number of vegetables that have the potential to be numerated. Using generalized linear modelling we identified which attributes were linear predictors of an outlet's healthiness assessment from nutritional researchers. The availability of water, salad, and the diversity of vegetables were positively associated with academic researchers' assessment of an outlet's healthiness, whereas the availability of chips, desserts, and multiple meal sizes were negatively associated. This study shows promise for the feasibility of an objective measure of healthiness that could be applied to all outlet listings on Just Eat and other digital food outlet aggregation platforms. However, further research is required to assess the metric's validity, its desirability and value to users, and ultimately its potential influence on food choice behaviour.

Ecology of Freshwater Fish, Jun 1, 2009

– Burbot Lota lota are of global conservation concern particularly near the southern extent of ... more – Burbot Lota lota are of global conservation concern particularly near the southern extent of the species range. Populations in small streams lack quantitative descriptions of resource selection. Microhabitat and reach‐scale habitat were surveyed at occupied and unoccupied locations. Data were analyzed with logistic regression to develop resource selection function models which predicted the probability of occurrence and abundance categories for microhabitat and reach‐scale habitat, respectively. Information‐theoretic model selection methods were used in an exploratory context, and four competing models were multi‐model averaged to create a microhabitat resource selection function. The sum of Akaike’s Information Criterion weights across the four competing models indicated that substrate type, substrate embeddedness, and depth were equally the most important microhabitat explanatory variables. At the reach scale, high correlation among explanatory variables precluded multivariate model development. Stream‐reach gradient was the most supported univariate model. Three additional models competed as important; mean summer temperature, sinuosity, and dominant substrate type. The created resource selection functions can be used in ranking potential translocation sites, used in instream flow assessments, and provide habitat selection information that can provide context for habitat management decisions.

Journal of Evolutionary Biology, Nov 2, 2010

Journal of Freshwater Ecology, Mar 1, 2010

We studied the population structure and diet of burbot (Lota lota) listed as stateendangered and ... more We studied the population structure and diet of burbot (Lota lota) listed as stateendangered and inhabiting small streams near the southern extent of the species' North American range. The size structure was truncated, with a mean total length of 191 mm and range of 84-356 mm. A subsample of individuals (n=32) were euthanized, and age estimates from otoliths revealed surprisingly short lifespans (maximum age of five years). An age-length key was then used to assign ages proportionately to the larger sample. and 80% were estimated to have been age 2 and age 3. Burbot stomach contents were removed with gastric lavage from 120 individuals during summer sampling that occurred at fourhour intervals for 24 h. Burbot specialized on Ephemeroptera, and consumed a variety of other invertebrate prey; surprisingly. fish were only found in three individuals. While similar to other reports of burbot in small streams, (e.g. small body sizes, earlier maturation, short-lifespan, invertebrate-centered diet) the population demographics were considerably different from 'typical' burbot populations occurring in lakes, large rivers, and reservoirs.

Transactions of The American Fisheries Society, Sep 1, 2011

We monitored survival and tag loss among Moapa White River springfish Crenichthys baileyi moapae ... more We monitored survival and tag loss among Moapa White River springfish Crenichthys baileyi moapae that were surgically implanted with passive integrated transponder (PIT; 9 × 2 mm) tags. The fish used in the study ranged from 40 to 67 mm in total length and from 1.0 to 6.5 g in mass; the PIT tag: body weight ratios were 1.0–6.1%. Fish were held for 41 d in live cages within a small, warm desert stream. Survival did not differ between untagged control fish (94.5%) and tagged fish (95.6%). Survival did not appear to be influenced by fish size or PIT tag: body weight ratio, but the small number of fish that died precluded a detailed analysis. Tag retention was 100% among the 86 fish that survived over the 41 d. Our results suggest that surgically implanting 9‐mm PIT tags into Moapa White River springfish as small as 40 mm is an effective method for marking them because it has minimal impacts on survival and tag retention is high. More work is needed on the effects of PIT tagging on growth and other performance metrics of springfish and other small desert fishes.

Journal of Biological Chemistry, Mar 1, 2018

Edited by Joseph M. Jez Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable the im... more Edited by Joseph M. Jez Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable the immune system to recognize and respond to pathogen attack. An early consequence of immune activation is transcriptional reprogramming, and some NLRs have been shown to act in the nucleus and interact with transcription factors. The Rx1 NLR protein of potato is further able to bind and distort double-stranded DNA. However, Rx1 host targets that support a role for Rx1 in transcriptional reprogramming at DNA are unknown. Here, we report a functional interaction between Rx1 and NbGlk1, a Golden2-like transcription factor. Rx1 binds to NbGlk1 in vitro and in planta. NbGlk1 binds to known Golden2like consensus DNA sequences. Rx1 reduces the binding affinity of NbGlk1 for DNA in vitro. NbGlk1 activates cellular responses to potato virus X, whereas Rx1 associates with NbGlk1 and prevents its assembly on DNA in planta unless activated by PVX. This study provides new mechanistic insight into how an NLR can coordinate an immune signaling response at DNA following pathogen perceptions.

Evolution, Jan 17, 2012

The mechanics of speciation with gene flow are still unclear. Disparity among genes in population... more The mechanics of speciation with gene flow are still unclear. Disparity among genes in population differentiation (F ST) between diverging species is often interpreted as evidence for semipermeable species boundaries, with selection preventing "key" genes from introgressing despite ongoing gene flow. However, F ST can remain high before it reaches equilibrium between the lineage sorting of species divergence and the homogenizing effects of gene flow (via secondary contact). Thus, when interpreting F ST , the dynamics of drift, gene flow, and selection need to be taken into account. We illustrate this view with a multigenic analyses of gene flow and selection in three closely related Silene species, S. latifolia, S. dioica, and S. diclinis. We report that although S. diclinis appears to have evolved in allopatry, isolation with (bidirectional) gene flow between S. latifolia and S. dioica is likely, perhaps as a result of parapatric speciation followed by more extensive sympatry. Interestingly, we detected the signatures of apparently independent instances of positive selection at the same locus in S. latifolia and S. dioica. Despite gene flow between the species, the adaptive alleles have not crossed the species boundary, suggesting that this gene has independently undergone species-specific (diversifying or parallel) selection.

The family Meliaceace contains some of the world's finest grade cabinet timbers. These includ... more The family Meliaceace contains some of the world's finest grade cabinet timbers. These include the Honduran mahogany (Swietenia macrophylla), West Indian mahogany (S. mahogani), Ugandan mahogany (Entandrophragma sp.), Asian Chukrasia (Chukrasia tabularis) and the Australian red cedar or Indian Toon (T. ciliata). Timber of T. ciliata was exported from Australia to Calcutta, India, in 1795 just seven years after the first British settlement was established in Sydney, thus becoming Australia's first export. The harvesting of this species was very important to the economy of the early European settlement and the timber getters helped open up the coastal forests for later agricultural activities (Boland, 1997). The species was also arguably the first Australian plant species to have conservation measures placed upon it (Boland, 1997) when it was realised that the species was rapidly disappearing in areas near Sydney. In India, thirty years ago, timber of T. ciliata was said to be...

International Journal of Environmental Research and Public Health, 2020

Digital food ordering platforms are used by millions across the world and provide easy access to ... more Digital food ordering platforms are used by millions across the world and provide easy access to takeaway fast-food that is broadly, though not exclusively, characterised as energy dense and nutrient poor. Outlets are routinely rated for hygiene, but not for their healthiness. Nutritional information is mandatory in pre-packaged foods, with many companies voluntarily using traffic light labels to support making healthier choices. We wanted to identify a feasible universal method to objectively score takeaway fast-food outlets listed on Just Eat that could provide users with an accessible rating that can infer an outlet’s ‘healthiness’. Using a sample of takeaway outlets listed on Just Eat, we obtained four complete assessments by nutrition researchers of each outlet’s healthiness to create a cumulative score that ranged from 4 to 12. We then identified and manually extracted nutritional attributes from each outlet’s digital menu, e.g., number of vegetables that have the potential to...

Proceedings of the Annual Conference of CAIS / Actes du congrès annuel de l'ACSI, 2013

While the dramatic growth of book superstores has been of great concern to public libraries, ther... more While the dramatic growth of book superstores has been of great concern to public libraries, there has been little serious research about what people actually do in bookstores. How much are their behaviours like those that typically occur in libraries? To what extent are they different? To answer these questions an unobtrusive observational study is underway at three Chapters bookstores in two large Ontario cities.

Proceedings of the Annual Conference of CAIS / Actes du congrès annuel de l'ACSI, 2013

Unobtrusive observation in nine sites in two public libraries in Southern Ontario explored user c... more Unobtrusive observation in nine sites in two public libraries in Southern Ontario explored user compliance with posted rules of conduct. With the exception of children who were frequently loud and rambunctious, most users followed the rules. This finding is consistent with Goffman’s idea that behaviour in public places is governed by normative assumptions of public order.L’observation non obstructive effectuée dans neuf sites de deux bibliothèques publiques du sud de l’Ontario a examiné la conformité de l’utilisateur avec les règles de conduite affichées. À l’exception des enfants qui étaient fréquemment bruyants et querelleurs, la plupart des utilisateurs ont suivi le règlement. Ces résultats sont conformes avec l’idée de Goffman affirmant que le comportement dans les endroits publics est régi par des conventions normatives au sujet de l’ordre public.