Transferrins are iron-binding proteins that are involved in iron storage and resistance to bacter... more Transferrins are iron-binding proteins that are involved in iron storage and resistance to bacterial disease. Previous work has shown that nonsynonymous-to-synonymous-site substitution ratios (d n /d s ratios) between transferrin genes from some salmonid species were significantly greater than 1.0, providing evidence for positive selection at the transferrin gene. The purpose of the current study was to put these earlier results in a broader evolutionary context by examining variation among 25 previously published transferrin sequences from fish, amphibians, and mammals. The results of the study show that evidence for positive selection at transferrin is limited to salmonids-d n /d s ratios estimated for nonsalmonid lineages were generally less than 1.0. Within the salmonids, ϳ13% of the transferrin codon sites are estimated to be subject to positive selection, with an estimated d n /d s ratio of ϳ7. The threedimensional locations of some of the selected sites were inferred by comparing these sites to homologous sites in the bovine lactoferrin crystallographic structure. The selected sites generally fall on the outside of the molecule, within and near areas that are bound by transferrin-binding proteins from human pathogenic bacteria. The physical locations of sites estimated to be subject to positive selection support previous speculation that competition for iron from pathogenic bacteria could be the source of positive selection.
Canadian Journal of Fisheries and Aquatic Sciences, 2014
Oncorhynchus mykiss form partially migratory populations with anadromous fish that undergo marine... more Oncorhynchus mykiss form partially migratory populations with anadromous fish that undergo marine migrations and residents that complete their life cycle in fresh water. Many populations' anadromous components are threatened or endangered, prompting interest in understanding ecological and evolutionary processes underlying anadromy and residency. In this paper, we synthesize information to better understand genetic and environmental influences on O. mykiss life histories, identify critical knowledge gaps, and suggest next steps. Anadromy and residency appear to reflect interactions among genetics, individual condition, and environmental influences. First, an increasing body of literature suggests that anadromous and resident individuals differ in the expression of genes related to growth, smoltification, and metabolism. Second, the literature supports the conditional strategy theory, where individuals adopt a life history pattern based on their conditional status relative to genetic thresholds along with ultimate effects of size and age at maturation and iteroparity. However, except for a generally positive association between residency and high lipid content plus a large attainable size in fresh water, the effects of body size and growth are inconsistent. Thus, individuals can exhibit plasticity in variable environments. Finally, patterns in anadromy and residency among and within populations suggested a wide range of possible environmental influences at different life stages, from freshwater temperature to marine survival. Although we document a number of interesting correlations, direct tests of mechanisms are scarce and little data exist on the extent of residency and anadromy. Consequently, we identified as many data gaps as conclusions, leaving ample room for future research.
Canadian Journal of Fisheries and Aquatic Sciences, 2012
The transition from dispersal into unoccupied habitat to the establishment of a self-sustaining n... more The transition from dispersal into unoccupied habitat to the establishment of a self-sustaining new population depends on the dynamics of the source and recipient populations, and the environmental conditions that facilitate or hinder exchange and successful reproduction. We used population growth rate, inter-annual variability estimates, habitat condition and size, hydrologic data, and an estimated dispersal effect to determine when colonizing
Global climate change during the Late Pleistocene periodically encroached and then released habit... more Global climate change during the Late Pleistocene periodically encroached and then released habitat during the glacial cycles, causing range expansions and contractions in some species. These dynamics have played a major role in geographic radiations, diversification and speciation. We investigate these dynamics in the most widely distributed of marine mammals, the killer whale (Orcinus orca), using a global dataset of over 450 samples. This marine top predator inhabits coastal and pelagic ecosystems ranging from the ice edge to the tropics, often exhibiting ecological, behavioral and morphological variation suggestive of local adaptation accompanied by reproductive isolation. Results suggest a rapid global radiation occurred over the last 350,000 years. Based on habitat models, we estimated there was only a 15% global contraction of core suitable habitat during the Last Glacial Maximum, and the resources appeared to sustain a constant global effective female population size through...
For widely distributed species at risk, such as Pacific salmon (Oncorhynchus spp.), habitat monit... more For widely distributed species at risk, such as Pacific salmon (Oncorhynchus spp.), habitat monitoring is both essential and challenging. Only recently have widespread monitoring programs been implemented for salmon habitat in the Pacific Northwest. Remote sensing data, such as Landsat images, are therefore a useful way to evaluate trends prior to the advent of species-specific habitat monitoring programs. We used annual (1986-2008) land cover maps created from Landsat images via automated algorithms (LandTrendr) to evaluate trends in developed (50-100% impervious) land cover in areas adjacent to five types of habitat utilized by Chinook salmon (O. tshawytscha) in the Puget Sound region of Washington State, U.S.A. For the region as a whole, we found significant increases in developed land cover adjacent to each of the habitat types evaluated (nearshore, estuary, mainstem channel, tributary channel, and floodplain), but the increases were small (<1% total increase from 1986 to 2008). For each habitat type, the increasing trend changed during the time series. In nearshore, mainstem, and floodplain areas, the rate of increase in developed land cover slowed in the latter portion of the time series, while the opposite occurred in estuary and tributary areas. Watersheds that were already highly developed in 1986 tended to have higher rates of development than initially less developed watersheds. Overall, our results suggest that developed land cover in areas adjacent to Puget Sound salmon habitat has increased only slightly since 1986 and that the rate of change has slowed near some key habitat types, although this has occurred within the context of a degraded baseline condition.
Methods and Technologies in Fish Biology and Fisheries, 2007
Abstract: For over a century, aquaculture of Pacific salmon has been used to provide increased ha... more Abstract: For over a century, aquaculture of Pacific salmon has been used to provide increased harvest opportunities and to mitigate reductions in natural populations due to factors such as habitat destruction, overharvest, and blockage of migratory routes. More recently, ...
Numerous substrates are available for the detection of b-ga- lactosidase, the most common being o... more Numerous substrates are available for the detection of b-ga- lactosidase, the most common being ortho-nitrophenyl-b-D- galactopyranoside (ONPG), which releases yellowo-nitrophe- nol upon hydrolysis (7). Fluorogenic substrates have also been used with labels such as resorufin, fluorescein, and 4-methyl- umbelliferone (2, 9). A major limitation of most of these sub- strates is that the aglycone released by hydrolysis has a tend- ency to diffuse widely, and they are therefore not suited to incorporation into agar plates. Because of these limitations, chromogenic substrates which producenondiffusibleproductshavebeendevelopedforincor- poration into agar media (8). Such substrates include galacto- sides of indoxyl and its halogenated derivatives, such as 5-bro- mo-4-chloro-3-indolyl-b-D-galactopyranoside (X-Gal) (6). Although these substrates are highly effective, their prepara- tion is not straightforward and they are consequently very expensive. We describe the synthesis of two new subs...
Cephalexin-aztreonam-arabinose agar (CAA), a new selective agar, was examined in comparison with ... more Cephalexin-aztreonam-arabinose agar (CAA), a new selective agar, was examined in comparison with nalidixic acid-colistin agar for the differentiation of Enterococcus faecium from other enterococci and the ability to isolate the organism from feces. Two hundred sixteen enterococcus isolates and a variety of gram-positive and gram-negative control strains were inoculated onto both media. All control strains of E. faecium were easily differentiated from Enterococcus faecalis and Enterococcus durans on the basis of arabinose fermentation on CAA. Differentiation of E. faecium from other enterococci or Streptococcus bovis was not possible on nalidixic acid-colistin agar. Increased isolation of E. faecium was demonstrated on CAA when both media were compared for the isolation of the organism from feces. CAA has been shown to possess excellent differential and selective features allowing the simple and effective isolation of E. faecium from heavily contaminated sites.
We describe a new chromogenic agar medium, ABC medium (alphabeta-chromogenic medium), which inclu... more We describe a new chromogenic agar medium, ABC medium (alphabeta-chromogenic medium), which includes two substrates, 3, 4-cyclohexenoesculetin-beta-D-galactoside and 5-bromo-4-chloro-3-indolyl-alpha-D-galactopyranoside, to facilitate the selective isolation of Salmonella spp. This medium exploits the fact that Salmonella spp. may be distinguished from other members of the family Enterobacteriaceae by the presence of alpha-galactosidase activity in the absence of beta-galactosidase activity. A total of 1, 022 strains of Salmonella spp. and 300 other gram-negative strains were inoculated onto this medium. Of these, 1,019 (99.7%) strains of Salmonella spp. produced a characteristic green colony, whereas only 1 strain (0.33%) of non-Salmonella produced a green colony. A total of 283 stool samples were cultured onto desoxycholate citrate (DC) agar and ABC medium by direct inoculation and after selective enrichment in selenite broth. Overall, the sensitivity and specificity were superior ...
Two rapid (1-h) assays for the detection of Staphylococcus aureus staphylocoagulase were develope... more Two rapid (1-h) assays for the detection of Staphylococcus aureus staphylocoagulase were developed by using the fluorogenic thrombin substrates N-t-boc-Val-Pro-Arg-7-amido-4-methylcoumarin (VPA) and N-t-boc-beta-benzyl-Asp-Pro-Arg-7-amido-4-methylocoumarin (BB). The assays were compared to the tube coagulase test and latex agglutination (LA) (Sanofi Diagnostics Pasteur, Guildford, Surrey, United Kingdom) by using 406 clinical isolates of staphylococci, and they produced positive and negative predictive values of 99.2 and 99. 1% for LA, 98.9 and 92.7% for VPA, and 98.9 and 99.1% for BB. Fluorescent assays used colonies from solid media, thereby eliminating the need for broth cultures, and were performed in microtiter trays, thus making them suitable for large-scale screening.
Myriad human activities increasingly threaten the existence of many species. A variety of conserv... more Myriad human activities increasingly threaten the existence of many species. A variety of conservation interventions such as habitat restoration, protected areas, and captive breeding have been used to prevent extinctions. Evaluating the effectiveness of these interventions requires appropriate statistical methods, given the quantity and quality of available data. Historically, analysis of variance has been used with some form of predetermined before-after control-impact design to estimate the effects of large-scale experiments or conservation interventions. However, ad hoc retrospective study designs or the presence of random effects at multiple scales may preclude the use of these tools. We evaluated the effects of a large-scale supplementation program on the density of adult Chinook salmon Oncorhynchus tshawytscha from the Snake River basin in the northwestern United States currently listed under the U.S. Endangered Species Act. We analyzed 43 years of data from 22 populations, accounting for random effects across time and space using a form of Bayesian hierarchical time-series model common in analyses of financial markets. We found that varying degrees of supplementation over a period of 25 years increased the density of natural-origin adults, on average, by 0-8% relative to nonsupplementation years. Thirty-nine of the 43 year effects were at least two times larger in magnitude than the mean supplementation effect, suggesting common environmental variables play a more important role in driving interannual variability in adult density. Additional residual variation in density varied considerably across the region, but there was no systematic difference between supplemented and reference populations. Our results demonstrate the power of hierarchical Bayesian models to detect the diffuse effects of management interventions and to quantitatively describe the variability of intervention success. Nevertheless, our study could not address whether ecological factors (e.g., competition) were more important than genetic considerations (e.g., inbreeding depression) in determining the response to supplementation.
We describe the synthesis of two new substrates for the detection of beta-galactosidase and evalu... more We describe the synthesis of two new substrates for the detection of beta-galactosidase and evaluate their performance in comparison with that of 5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside (X-Gal). Of 171 Enterobacteriaceae strains that were able to hydrolyze X-Gal, 166 (97.1%) also hydrolyzed cyclohexenoesculetin-beta-D-galactoside whereas only 96 (56.1%) showed evidence of hydrolysis of 8-hydroxyquinoline-beta-D-galactoside. No false-positive results were observed with either substrate.
Individuals with chronic excessive alcohol ingestion are put at the risk of acute and chronic pan... more Individuals with chronic excessive alcohol ingestion are put at the risk of acute and chronic pancreatitis. Underlying molecular mechanisms are unknown. Differential gene expression in the pancreas was profiled using mRNA differential display by comparison between control and ethanol-consuming rats. Male Wistar rats were fed with diets containing 6.7% (vol/vol) ethanol for 4 wk. A cDNA tag that was overexpressed in the pancreas of rats fed ethanol was isolated. A 723-bp cDNA was cloned from a rat pancreatic cDNA library, which encodes a novel rat mitochondrial ATP synthase subunit 9, isoform 3 (ATP5G3), which is homologous to a human ATP5G3 gene. Real-time PCR demonstrated that all three nuclear gene isoforms (ATP5G1, ATP5G2, and ATP5G3) were consistently upregulated in the pancreas of alcohol-consuming rats, parallel with mitochondrial injury. The cellular response to mitochondrial damage and metabolic stress may reflect an adaptive process for mitochondrial repair in pancreatic ac...
We describe a new chromogenic agar medium, ABC medium (alphabeta-chromogenic medium), which inclu... more We describe a new chromogenic agar medium, ABC medium (alphabeta-chromogenic medium), which includes two substrates, 3, 4-cyclohexenoesculetin-beta-D-galactoside and 5-bromo-4-chloro-3-indolyl-alpha-D-galactopyranoside, to facilitate the selective isolation of Salmonella spp. This medium exploits the fact that Salmonella spp. may be distinguished from other members of the family Enterobacteriaceae by the presence of alpha-galactosidase activity in the absence of beta-galactosidase activity. A total of 1, 022 strains of Salmonella spp. and 300 other gram-negative strains were inoculated onto this medium. Of these, 1,019 (99.7%) strains of Salmonella spp. produced a characteristic green colony, whereas only 1 strain (0.33%) of non-Salmonella produced a green colony. A total of 283 stool samples were cultured onto desoxycholate citrate (DC) agar and ABC medium by direct inoculation and after selective enrichment in selenite broth. Overall, the sensitivity and specificity were superior ...
Proceedings of The National Academy of Sciences, 1999
We report DNA and predicted protein sequence similarities, implying homology, among genes of doub... more We report DNA and predicted protein sequence similarities, implying homology, among genes of double-stranded DNA (dsDNA) bacteriophages and prophages spanning a broad phylogenetic range of host bacteria. The sequence matches reported here establish genetic connections, not always direct, among the lambdoid phages of Escherichia coli, phage phiC31 of Streptomyces, phages of Mycobacterium, a previously unrecognized cryptic prophage, phiflu, in the Haemophilus influenzae genome, and two small prophage-like elements, phiRv1 and phiRv2, in the genome of Mycobacterium tuberculosis. The results imply that these phage genes, and very possibly all of the dsDNA tailed phages, share common ancestry. We propose a model for the genetic structure and dynamics of the global phage population in which all dsDNA phage genomes are mosaics with access, by horizontal exchange, to a large common genetic pool but in which access to the gene pool is not uniform for all phage.
In this paper we explore the question of whether additional benefits can be derived from providin... more In this paper we explore the question of whether additional benefits can be derived from providing formative feedback on students' explanations given the difficulties of accurately assessing them automatically. We provide a preliminary evaluation of an approach in which students assist in interpreting their own explanations and we lay out our plans for evaluating the effectiveness of a natural-language intelligent tutoring system's feedback to that interpretation effort. The preliminary evaluation suggests that students respond well to the approach. While their interpretation assistance may be similar to an automated explanation matcher, they continue to provide explanations throughout their interactions.
The phenotypic consequences of expression quantitative trait loci (eQTLs) are presumably due to t... more The phenotypic consequences of expression quantitative trait loci (eQTLs) are presumably due to their effects on protein expression levels. Yet the impact of genetic variation, including eQTLs, on protein levels remains poorly understood. To address this, we mapped genetic variants that are associated with eQTLs, ribosome occupancy (rQTLs), or protein abundance (pQTLs). We found that most QTLs are associated with transcript expression levels, with consequent effects on ribosome and protein levels. However, eQTLs tend to have significantly reduced effect sizes on protein levels, which suggests that their potential impact on downstream phenotypes is often attenuated or buffered. Additionally, we identified a class of cis QTLs that affect protein abundance with little or no effect on messenger RNA or ribosome levels, which suggests that they may arise from differences in posttranslational regulation.
The phenotypic consequences of expression quantitative trait loci (eQTLs) are presumably due to t... more The phenotypic consequences of expression quantitative trait loci (eQTLs) are presumably due to their effects on protein expression levels. Yet the impact of genetic variation, including eQTLs, on protein levels remains poorly understood. To address this, we mapped genetic variants that are associated with eQTLs, ribosome occupancy (rQTLs), or protein abundance (pQTLs). We found that most QTLs are associated with transcript expression levels, with consequent effects on ribosome and protein levels. However, eQTLs tend to have significantly reduced effect sizes on protein levels, which suggests that their potential impact on downstream phenotypes is often attenuated or buffered. Additionally, we identified a class of cis QTLs that affect protein abundance with little or no effect on messenger RNA or ribosome levels, which suggests that they may arise from differences in posttranslational regulation.
Transferrins are iron-binding proteins that are involved in iron storage and resistance to bacter... more Transferrins are iron-binding proteins that are involved in iron storage and resistance to bacterial disease. Previous work has shown that nonsynonymous-to-synonymous-site substitution ratios (d n /d s ratios) between transferrin genes from some salmonid species were significantly greater than 1.0, providing evidence for positive selection at the transferrin gene. The purpose of the current study was to put these earlier results in a broader evolutionary context by examining variation among 25 previously published transferrin sequences from fish, amphibians, and mammals. The results of the study show that evidence for positive selection at transferrin is limited to salmonids-d n /d s ratios estimated for nonsalmonid lineages were generally less than 1.0. Within the salmonids, ϳ13% of the transferrin codon sites are estimated to be subject to positive selection, with an estimated d n /d s ratio of ϳ7. The threedimensional locations of some of the selected sites were inferred by comparing these sites to homologous sites in the bovine lactoferrin crystallographic structure. The selected sites generally fall on the outside of the molecule, within and near areas that are bound by transferrin-binding proteins from human pathogenic bacteria. The physical locations of sites estimated to be subject to positive selection support previous speculation that competition for iron from pathogenic bacteria could be the source of positive selection.
Canadian Journal of Fisheries and Aquatic Sciences, 2014
Oncorhynchus mykiss form partially migratory populations with anadromous fish that undergo marine... more Oncorhynchus mykiss form partially migratory populations with anadromous fish that undergo marine migrations and residents that complete their life cycle in fresh water. Many populations' anadromous components are threatened or endangered, prompting interest in understanding ecological and evolutionary processes underlying anadromy and residency. In this paper, we synthesize information to better understand genetic and environmental influences on O. mykiss life histories, identify critical knowledge gaps, and suggest next steps. Anadromy and residency appear to reflect interactions among genetics, individual condition, and environmental influences. First, an increasing body of literature suggests that anadromous and resident individuals differ in the expression of genes related to growth, smoltification, and metabolism. Second, the literature supports the conditional strategy theory, where individuals adopt a life history pattern based on their conditional status relative to genetic thresholds along with ultimate effects of size and age at maturation and iteroparity. However, except for a generally positive association between residency and high lipid content plus a large attainable size in fresh water, the effects of body size and growth are inconsistent. Thus, individuals can exhibit plasticity in variable environments. Finally, patterns in anadromy and residency among and within populations suggested a wide range of possible environmental influences at different life stages, from freshwater temperature to marine survival. Although we document a number of interesting correlations, direct tests of mechanisms are scarce and little data exist on the extent of residency and anadromy. Consequently, we identified as many data gaps as conclusions, leaving ample room for future research.
Canadian Journal of Fisheries and Aquatic Sciences, 2012
The transition from dispersal into unoccupied habitat to the establishment of a self-sustaining n... more The transition from dispersal into unoccupied habitat to the establishment of a self-sustaining new population depends on the dynamics of the source and recipient populations, and the environmental conditions that facilitate or hinder exchange and successful reproduction. We used population growth rate, inter-annual variability estimates, habitat condition and size, hydrologic data, and an estimated dispersal effect to determine when colonizing
Global climate change during the Late Pleistocene periodically encroached and then released habit... more Global climate change during the Late Pleistocene periodically encroached and then released habitat during the glacial cycles, causing range expansions and contractions in some species. These dynamics have played a major role in geographic radiations, diversification and speciation. We investigate these dynamics in the most widely distributed of marine mammals, the killer whale (Orcinus orca), using a global dataset of over 450 samples. This marine top predator inhabits coastal and pelagic ecosystems ranging from the ice edge to the tropics, often exhibiting ecological, behavioral and morphological variation suggestive of local adaptation accompanied by reproductive isolation. Results suggest a rapid global radiation occurred over the last 350,000 years. Based on habitat models, we estimated there was only a 15% global contraction of core suitable habitat during the Last Glacial Maximum, and the resources appeared to sustain a constant global effective female population size through...
For widely distributed species at risk, such as Pacific salmon (Oncorhynchus spp.), habitat monit... more For widely distributed species at risk, such as Pacific salmon (Oncorhynchus spp.), habitat monitoring is both essential and challenging. Only recently have widespread monitoring programs been implemented for salmon habitat in the Pacific Northwest. Remote sensing data, such as Landsat images, are therefore a useful way to evaluate trends prior to the advent of species-specific habitat monitoring programs. We used annual (1986-2008) land cover maps created from Landsat images via automated algorithms (LandTrendr) to evaluate trends in developed (50-100% impervious) land cover in areas adjacent to five types of habitat utilized by Chinook salmon (O. tshawytscha) in the Puget Sound region of Washington State, U.S.A. For the region as a whole, we found significant increases in developed land cover adjacent to each of the habitat types evaluated (nearshore, estuary, mainstem channel, tributary channel, and floodplain), but the increases were small (<1% total increase from 1986 to 2008). For each habitat type, the increasing trend changed during the time series. In nearshore, mainstem, and floodplain areas, the rate of increase in developed land cover slowed in the latter portion of the time series, while the opposite occurred in estuary and tributary areas. Watersheds that were already highly developed in 1986 tended to have higher rates of development than initially less developed watersheds. Overall, our results suggest that developed land cover in areas adjacent to Puget Sound salmon habitat has increased only slightly since 1986 and that the rate of change has slowed near some key habitat types, although this has occurred within the context of a degraded baseline condition.
Methods and Technologies in Fish Biology and Fisheries, 2007
Abstract: For over a century, aquaculture of Pacific salmon has been used to provide increased ha... more Abstract: For over a century, aquaculture of Pacific salmon has been used to provide increased harvest opportunities and to mitigate reductions in natural populations due to factors such as habitat destruction, overharvest, and blockage of migratory routes. More recently, ...
Numerous substrates are available for the detection of b-ga- lactosidase, the most common being o... more Numerous substrates are available for the detection of b-ga- lactosidase, the most common being ortho-nitrophenyl-b-D- galactopyranoside (ONPG), which releases yellowo-nitrophe- nol upon hydrolysis (7). Fluorogenic substrates have also been used with labels such as resorufin, fluorescein, and 4-methyl- umbelliferone (2, 9). A major limitation of most of these sub- strates is that the aglycone released by hydrolysis has a tend- ency to diffuse widely, and they are therefore not suited to incorporation into agar plates. Because of these limitations, chromogenic substrates which producenondiffusibleproductshavebeendevelopedforincor- poration into agar media (8). Such substrates include galacto- sides of indoxyl and its halogenated derivatives, such as 5-bro- mo-4-chloro-3-indolyl-b-D-galactopyranoside (X-Gal) (6). Although these substrates are highly effective, their prepara- tion is not straightforward and they are consequently very expensive. We describe the synthesis of two new subs...
Cephalexin-aztreonam-arabinose agar (CAA), a new selective agar, was examined in comparison with ... more Cephalexin-aztreonam-arabinose agar (CAA), a new selective agar, was examined in comparison with nalidixic acid-colistin agar for the differentiation of Enterococcus faecium from other enterococci and the ability to isolate the organism from feces. Two hundred sixteen enterococcus isolates and a variety of gram-positive and gram-negative control strains were inoculated onto both media. All control strains of E. faecium were easily differentiated from Enterococcus faecalis and Enterococcus durans on the basis of arabinose fermentation on CAA. Differentiation of E. faecium from other enterococci or Streptococcus bovis was not possible on nalidixic acid-colistin agar. Increased isolation of E. faecium was demonstrated on CAA when both media were compared for the isolation of the organism from feces. CAA has been shown to possess excellent differential and selective features allowing the simple and effective isolation of E. faecium from heavily contaminated sites.
We describe a new chromogenic agar medium, ABC medium (alphabeta-chromogenic medium), which inclu... more We describe a new chromogenic agar medium, ABC medium (alphabeta-chromogenic medium), which includes two substrates, 3, 4-cyclohexenoesculetin-beta-D-galactoside and 5-bromo-4-chloro-3-indolyl-alpha-D-galactopyranoside, to facilitate the selective isolation of Salmonella spp. This medium exploits the fact that Salmonella spp. may be distinguished from other members of the family Enterobacteriaceae by the presence of alpha-galactosidase activity in the absence of beta-galactosidase activity. A total of 1, 022 strains of Salmonella spp. and 300 other gram-negative strains were inoculated onto this medium. Of these, 1,019 (99.7%) strains of Salmonella spp. produced a characteristic green colony, whereas only 1 strain (0.33%) of non-Salmonella produced a green colony. A total of 283 stool samples were cultured onto desoxycholate citrate (DC) agar and ABC medium by direct inoculation and after selective enrichment in selenite broth. Overall, the sensitivity and specificity were superior ...
Two rapid (1-h) assays for the detection of Staphylococcus aureus staphylocoagulase were develope... more Two rapid (1-h) assays for the detection of Staphylococcus aureus staphylocoagulase were developed by using the fluorogenic thrombin substrates N-t-boc-Val-Pro-Arg-7-amido-4-methylcoumarin (VPA) and N-t-boc-beta-benzyl-Asp-Pro-Arg-7-amido-4-methylocoumarin (BB). The assays were compared to the tube coagulase test and latex agglutination (LA) (Sanofi Diagnostics Pasteur, Guildford, Surrey, United Kingdom) by using 406 clinical isolates of staphylococci, and they produced positive and negative predictive values of 99.2 and 99. 1% for LA, 98.9 and 92.7% for VPA, and 98.9 and 99.1% for BB. Fluorescent assays used colonies from solid media, thereby eliminating the need for broth cultures, and were performed in microtiter trays, thus making them suitable for large-scale screening.
Myriad human activities increasingly threaten the existence of many species. A variety of conserv... more Myriad human activities increasingly threaten the existence of many species. A variety of conservation interventions such as habitat restoration, protected areas, and captive breeding have been used to prevent extinctions. Evaluating the effectiveness of these interventions requires appropriate statistical methods, given the quantity and quality of available data. Historically, analysis of variance has been used with some form of predetermined before-after control-impact design to estimate the effects of large-scale experiments or conservation interventions. However, ad hoc retrospective study designs or the presence of random effects at multiple scales may preclude the use of these tools. We evaluated the effects of a large-scale supplementation program on the density of adult Chinook salmon Oncorhynchus tshawytscha from the Snake River basin in the northwestern United States currently listed under the U.S. Endangered Species Act. We analyzed 43 years of data from 22 populations, accounting for random effects across time and space using a form of Bayesian hierarchical time-series model common in analyses of financial markets. We found that varying degrees of supplementation over a period of 25 years increased the density of natural-origin adults, on average, by 0-8% relative to nonsupplementation years. Thirty-nine of the 43 year effects were at least two times larger in magnitude than the mean supplementation effect, suggesting common environmental variables play a more important role in driving interannual variability in adult density. Additional residual variation in density varied considerably across the region, but there was no systematic difference between supplemented and reference populations. Our results demonstrate the power of hierarchical Bayesian models to detect the diffuse effects of management interventions and to quantitatively describe the variability of intervention success. Nevertheless, our study could not address whether ecological factors (e.g., competition) were more important than genetic considerations (e.g., inbreeding depression) in determining the response to supplementation.
We describe the synthesis of two new substrates for the detection of beta-galactosidase and evalu... more We describe the synthesis of two new substrates for the detection of beta-galactosidase and evaluate their performance in comparison with that of 5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside (X-Gal). Of 171 Enterobacteriaceae strains that were able to hydrolyze X-Gal, 166 (97.1%) also hydrolyzed cyclohexenoesculetin-beta-D-galactoside whereas only 96 (56.1%) showed evidence of hydrolysis of 8-hydroxyquinoline-beta-D-galactoside. No false-positive results were observed with either substrate.
Individuals with chronic excessive alcohol ingestion are put at the risk of acute and chronic pan... more Individuals with chronic excessive alcohol ingestion are put at the risk of acute and chronic pancreatitis. Underlying molecular mechanisms are unknown. Differential gene expression in the pancreas was profiled using mRNA differential display by comparison between control and ethanol-consuming rats. Male Wistar rats were fed with diets containing 6.7% (vol/vol) ethanol for 4 wk. A cDNA tag that was overexpressed in the pancreas of rats fed ethanol was isolated. A 723-bp cDNA was cloned from a rat pancreatic cDNA library, which encodes a novel rat mitochondrial ATP synthase subunit 9, isoform 3 (ATP5G3), which is homologous to a human ATP5G3 gene. Real-time PCR demonstrated that all three nuclear gene isoforms (ATP5G1, ATP5G2, and ATP5G3) were consistently upregulated in the pancreas of alcohol-consuming rats, parallel with mitochondrial injury. The cellular response to mitochondrial damage and metabolic stress may reflect an adaptive process for mitochondrial repair in pancreatic ac...
We describe a new chromogenic agar medium, ABC medium (alphabeta-chromogenic medium), which inclu... more We describe a new chromogenic agar medium, ABC medium (alphabeta-chromogenic medium), which includes two substrates, 3, 4-cyclohexenoesculetin-beta-D-galactoside and 5-bromo-4-chloro-3-indolyl-alpha-D-galactopyranoside, to facilitate the selective isolation of Salmonella spp. This medium exploits the fact that Salmonella spp. may be distinguished from other members of the family Enterobacteriaceae by the presence of alpha-galactosidase activity in the absence of beta-galactosidase activity. A total of 1, 022 strains of Salmonella spp. and 300 other gram-negative strains were inoculated onto this medium. Of these, 1,019 (99.7%) strains of Salmonella spp. produced a characteristic green colony, whereas only 1 strain (0.33%) of non-Salmonella produced a green colony. A total of 283 stool samples were cultured onto desoxycholate citrate (DC) agar and ABC medium by direct inoculation and after selective enrichment in selenite broth. Overall, the sensitivity and specificity were superior ...
Proceedings of The National Academy of Sciences, 1999
We report DNA and predicted protein sequence similarities, implying homology, among genes of doub... more We report DNA and predicted protein sequence similarities, implying homology, among genes of double-stranded DNA (dsDNA) bacteriophages and prophages spanning a broad phylogenetic range of host bacteria. The sequence matches reported here establish genetic connections, not always direct, among the lambdoid phages of Escherichia coli, phage phiC31 of Streptomyces, phages of Mycobacterium, a previously unrecognized cryptic prophage, phiflu, in the Haemophilus influenzae genome, and two small prophage-like elements, phiRv1 and phiRv2, in the genome of Mycobacterium tuberculosis. The results imply that these phage genes, and very possibly all of the dsDNA tailed phages, share common ancestry. We propose a model for the genetic structure and dynamics of the global phage population in which all dsDNA phage genomes are mosaics with access, by horizontal exchange, to a large common genetic pool but in which access to the gene pool is not uniform for all phage.
In this paper we explore the question of whether additional benefits can be derived from providin... more In this paper we explore the question of whether additional benefits can be derived from providing formative feedback on students' explanations given the difficulties of accurately assessing them automatically. We provide a preliminary evaluation of an approach in which students assist in interpreting their own explanations and we lay out our plans for evaluating the effectiveness of a natural-language intelligent tutoring system's feedback to that interpretation effort. The preliminary evaluation suggests that students respond well to the approach. While their interpretation assistance may be similar to an automated explanation matcher, they continue to provide explanations throughout their interactions.
The phenotypic consequences of expression quantitative trait loci (eQTLs) are presumably due to t... more The phenotypic consequences of expression quantitative trait loci (eQTLs) are presumably due to their effects on protein expression levels. Yet the impact of genetic variation, including eQTLs, on protein levels remains poorly understood. To address this, we mapped genetic variants that are associated with eQTLs, ribosome occupancy (rQTLs), or protein abundance (pQTLs). We found that most QTLs are associated with transcript expression levels, with consequent effects on ribosome and protein levels. However, eQTLs tend to have significantly reduced effect sizes on protein levels, which suggests that their potential impact on downstream phenotypes is often attenuated or buffered. Additionally, we identified a class of cis QTLs that affect protein abundance with little or no effect on messenger RNA or ribosome levels, which suggests that they may arise from differences in posttranslational regulation.
The phenotypic consequences of expression quantitative trait loci (eQTLs) are presumably due to t... more The phenotypic consequences of expression quantitative trait loci (eQTLs) are presumably due to their effects on protein expression levels. Yet the impact of genetic variation, including eQTLs, on protein levels remains poorly understood. To address this, we mapped genetic variants that are associated with eQTLs, ribosome occupancy (rQTLs), or protein abundance (pQTLs). We found that most QTLs are associated with transcript expression levels, with consequent effects on ribosome and protein levels. However, eQTLs tend to have significantly reduced effect sizes on protein levels, which suggests that their potential impact on downstream phenotypes is often attenuated or buffered. Additionally, we identified a class of cis QTLs that affect protein abundance with little or no effect on messenger RNA or ribosome levels, which suggests that they may arise from differences in posttranslational regulation.
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Papers by Michael Ford