John Pollinger - Academia.edu (original) (raw)

Papers by John Pollinger

Research paper thumbnail of Correction: Batrachochytrium dendrobatidis Shows High Genetic Diversity and Ecological Niche Specificity among Haplotypes in the Maya Mountains of Belize

Research paper thumbnail of Optimization of an aqueous, commercial silicon nitride slurry for colloidal isopressing

Journal of the European Ceramic Society, 2002

A commercial Si3N4-based aqueous slurry (AS800) was processed to enable the forming of shapes via... more A commercial Si3N4-based aqueous slurry (AS800) was processed to enable the forming of shapes via a new method called colloidal isopressing. The as-received slurry was reformulated at pH 9–10 to contain 2 wt.% PEG-silane (N-[(triethoxysilyl)propyl]-O-polyethylene oxide urethane) and 0.5 M of either tetramethylammonium chloride or tetramethylammonium nitrate. The addition of the salt to an AS800 slurry formulated in the dispersed

Research paper thumbnail of A Physical Model for the Drying of Gelcast Ceramics

Journal of the American Ceramic Society, 2004

ABSTRACT

Research paper thumbnail of Pressure Sensitivity for Particle Packing of Aqueous Al2O3 Slurries vs Interparticle Potential

Journal of the American Ceramic Society, 1994

Research paper thumbnail of Metastable solid solution extension of mullite by rapid solidification

Journal of Materials Research, 1988

Research paper thumbnail of Evolutionary genomics of the dog and dog-like carnivores

Journal of Veterinary Behavior: Clinical Applications and Research, Volume 4, Issue 2, Pages 71, ... more Journal of Veterinary Behavior: Clinical Applications and Research, Volume 4, Issue 2, Pages 71, March 2009, Authors:Robert Wayne; John Pollinger; Klaus Koepfli; Carolyne Bardeleben;Melissa Gray; Carlos Bustamante; Bridgett vonHoldt; Nate Sutter; Elaine Ostrander. ...

Research paper thumbnail of A southern California freeway is a physical and social barrier to gene flow in carnivores

Research paper thumbnail of Disease and freeways drive genetic change in urban bobcat populations

Evolutionary Applications, 2014

Research paper thumbnail of Individual behaviors dominate the dynamics of an urban mountain lion population isolated by roads

Current biology : CB, Jan 8, 2014

Large carnivores can be particularly sensitive to the effects of habitat fragmentation on genetic... more Large carnivores can be particularly sensitive to the effects of habitat fragmentation on genetic diversity [1, 2]. The Santa Monica Mountains (SMMs), a large natural area within Greater Los Angeles, is completely isolated by urban development and the 101 freeway to the north. Yet the SMMs support a population of mountain lions (Puma concolor), a very rare example of a large carnivore persisting within the boundaries of a megacity. GPS locations of radio-collared lions indicate that freeways are a near-absolute barrier to movement. We genotyped 42 lions using 54 microsatellite loci and found that genetic diversity in SMM lions, prior to 2009, was lower than that for any population in North America except in southern Florida, where inbreeding depression led to reproductive failure [3-5]. We document multiple instances of father-daughter inbreeding and high levels of intraspecific strife, including the unexpected behavior of a male killing two of his offspring and a mate and his son k...

Research paper thumbnail of Hypoxia adaptations in the grey wolf (Canis lupus chanco) from Qinghai-Tibet Plateau

PLoS genetics, 2014

The Tibetan grey wolf (Canis lupus chanco) occupies habitats on the Qinghai-Tibet Plateau, a high... more The Tibetan grey wolf (Canis lupus chanco) occupies habitats on the Qinghai-Tibet Plateau, a high altitude (>3000 m) environment where low oxygen tension exerts unique selection pressure on individuals to adapt to hypoxic conditions. To identify genes involved in hypoxia adaptation, we generated complete genome sequences of nine Chinese wolves from high and low altitude populations at an average coverage of 25× coverage. We found that, beginning about 55,000 years ago, the highland Tibetan grey wolf suffered a more substantial population decline than lowland wolves. Positively selected hypoxia-related genes in highland wolves are enriched in the HIF signaling pathway (P = 1.57E-6), ATP binding (P = 5.62E-5), and response to an oxygen-containing compound (P≤5.30E-4). Of these positively selected hypoxia-related genes, three genes (EPAS1, ANGPT1, and RYR2) had at least one specific fixed non-synonymous SNP in highland wolves based on the nine genome data. Our re-sequencing studies ...

Research paper thumbnail of Pandemic A/H1N1/2009 influenza virus in Swine, Cameroon, 2010

Veterinary Microbiology, 2012

Research paper thumbnail of Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication

Research paper thumbnail of Genome sequence, comparative analysis and haplotype structure of the domestic dog

Research paper thumbnail of Low-coverage vaccination strategies for the conservation of endangered species

Research paper thumbnail of The role of geography and ecology in shaping the p hylogeography of the speckled hummingbird (Adelomyia melanogenys) in Ecuador

Molecular Phylogenetics and Evolution, 2007

Research paper thumbnail of Characterization of 15 tetranucleotide microsatellite markers in the ringtail ( Bassariscus astutus )

Molecular Ecology Resources, 2009

We characterized 15 polymorphic tetranucleotide microsatellite markers for the ringtail, Bassaris... more We characterized 15 polymorphic tetranucleotide microsatellite markers for the ringtail, Bassariscus astutus. We tested these loci in 21 individuals captured in Arizona and Texas and found six to 19 alleles per locus. Observed and expected heterozygosities ranged from 0.381 to 1.000 and from 0.381 to 0.941, respectively. All loci were in Hardy-Weinberg equilibrium, and none were in linkage disequilibrium. These markers may be used to investigate population genetics and mating patterns in this species.

Research paper thumbnail of Landscape genetics of California mule deer ( Odocoileus hemionus ): the roles of ecological and historical factors in generating differentiation

Research paper thumbnail of A novel assessment of population structure and gene flow in grey wolf populations of the Northern Rocky Mountains of the United States

Research paper thumbnail of The genealogy and genetic viability of reintroduced Yellowstone grey wolves

Research paper thumbnail of Rapid influenza A detection and quantitation in birds using a one-step real-time reverse transcriptase PCR and High Resolution Melting

Journal of Virological Methods, 2011

Efficient influenza A viral surveillance of wild and domestic birds requires rapid viral detectio... more Efficient influenza A viral surveillance of wild and domestic birds requires rapid viral detection and quantitation of high and low quality samples. Current influenza A qPCR-based detection protocols specified by CDC, OIE and USDA utilize fluorogenic hydrolysis probe based real-time reverse transcription PCR (RRT-PCR) assays for detection and quantitation. The sequence diversity of this virus, even in the conserved matrix gene M1, makes primer and probe designs challenging. In this report it was determined that false RRT-PCR positives are possible with this method. This is particularly problematic when surveying non-cultured or inactivated avian tracheal and cloacal mucosal samples with low concentrations of virus and large proportions of background nucleic acids. This report presents a modification of a one-step RRT-PCR detection method for influenza A using SYBR green intercalating dye-based target amplification detection. High Resolution Melting (HRM), amplicon size quantitation and sequence verification is used to screen for non-target amplification (false positives). The resulting protocol has the sensitivity of hydrolysis probe methods, allows for flexible primer design and verification of target amplification, and provides high confidence in positive results. A multiplex subtype detection method using the RRT-PCR HRM assay is also demonstrated. Overall, this method is both time and cost effective while providing an extra measure of confidence in surveillance results through the implementation of target verification.

Research paper thumbnail of Correction: Batrachochytrium dendrobatidis Shows High Genetic Diversity and Ecological Niche Specificity among Haplotypes in the Maya Mountains of Belize

Research paper thumbnail of Optimization of an aqueous, commercial silicon nitride slurry for colloidal isopressing

Journal of the European Ceramic Society, 2002

A commercial Si3N4-based aqueous slurry (AS800) was processed to enable the forming of shapes via... more A commercial Si3N4-based aqueous slurry (AS800) was processed to enable the forming of shapes via a new method called colloidal isopressing. The as-received slurry was reformulated at pH 9–10 to contain 2 wt.% PEG-silane (N-[(triethoxysilyl)propyl]-O-polyethylene oxide urethane) and 0.5 M of either tetramethylammonium chloride or tetramethylammonium nitrate. The addition of the salt to an AS800 slurry formulated in the dispersed

Research paper thumbnail of A Physical Model for the Drying of Gelcast Ceramics

Journal of the American Ceramic Society, 2004

ABSTRACT

Research paper thumbnail of Pressure Sensitivity for Particle Packing of Aqueous Al2O3 Slurries vs Interparticle Potential

Journal of the American Ceramic Society, 1994

Research paper thumbnail of Metastable solid solution extension of mullite by rapid solidification

Journal of Materials Research, 1988

Research paper thumbnail of Evolutionary genomics of the dog and dog-like carnivores

Journal of Veterinary Behavior: Clinical Applications and Research, Volume 4, Issue 2, Pages 71, ... more Journal of Veterinary Behavior: Clinical Applications and Research, Volume 4, Issue 2, Pages 71, March 2009, Authors:Robert Wayne; John Pollinger; Klaus Koepfli; Carolyne Bardeleben;Melissa Gray; Carlos Bustamante; Bridgett vonHoldt; Nate Sutter; Elaine Ostrander. ...

Research paper thumbnail of A southern California freeway is a physical and social barrier to gene flow in carnivores

Research paper thumbnail of Disease and freeways drive genetic change in urban bobcat populations

Evolutionary Applications, 2014

Research paper thumbnail of Individual behaviors dominate the dynamics of an urban mountain lion population isolated by roads

Current biology : CB, Jan 8, 2014

Large carnivores can be particularly sensitive to the effects of habitat fragmentation on genetic... more Large carnivores can be particularly sensitive to the effects of habitat fragmentation on genetic diversity [1, 2]. The Santa Monica Mountains (SMMs), a large natural area within Greater Los Angeles, is completely isolated by urban development and the 101 freeway to the north. Yet the SMMs support a population of mountain lions (Puma concolor), a very rare example of a large carnivore persisting within the boundaries of a megacity. GPS locations of radio-collared lions indicate that freeways are a near-absolute barrier to movement. We genotyped 42 lions using 54 microsatellite loci and found that genetic diversity in SMM lions, prior to 2009, was lower than that for any population in North America except in southern Florida, where inbreeding depression led to reproductive failure [3-5]. We document multiple instances of father-daughter inbreeding and high levels of intraspecific strife, including the unexpected behavior of a male killing two of his offspring and a mate and his son k...

Research paper thumbnail of Hypoxia adaptations in the grey wolf (Canis lupus chanco) from Qinghai-Tibet Plateau

PLoS genetics, 2014

The Tibetan grey wolf (Canis lupus chanco) occupies habitats on the Qinghai-Tibet Plateau, a high... more The Tibetan grey wolf (Canis lupus chanco) occupies habitats on the Qinghai-Tibet Plateau, a high altitude (>3000 m) environment where low oxygen tension exerts unique selection pressure on individuals to adapt to hypoxic conditions. To identify genes involved in hypoxia adaptation, we generated complete genome sequences of nine Chinese wolves from high and low altitude populations at an average coverage of 25× coverage. We found that, beginning about 55,000 years ago, the highland Tibetan grey wolf suffered a more substantial population decline than lowland wolves. Positively selected hypoxia-related genes in highland wolves are enriched in the HIF signaling pathway (P = 1.57E-6), ATP binding (P = 5.62E-5), and response to an oxygen-containing compound (P≤5.30E-4). Of these positively selected hypoxia-related genes, three genes (EPAS1, ANGPT1, and RYR2) had at least one specific fixed non-synonymous SNP in highland wolves based on the nine genome data. Our re-sequencing studies ...

Research paper thumbnail of Pandemic A/H1N1/2009 influenza virus in Swine, Cameroon, 2010

Veterinary Microbiology, 2012

Research paper thumbnail of Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication

Research paper thumbnail of Genome sequence, comparative analysis and haplotype structure of the domestic dog

Research paper thumbnail of Low-coverage vaccination strategies for the conservation of endangered species

Research paper thumbnail of The role of geography and ecology in shaping the p hylogeography of the speckled hummingbird (Adelomyia melanogenys) in Ecuador

Molecular Phylogenetics and Evolution, 2007

Research paper thumbnail of Characterization of 15 tetranucleotide microsatellite markers in the ringtail ( Bassariscus astutus )

Molecular Ecology Resources, 2009

We characterized 15 polymorphic tetranucleotide microsatellite markers for the ringtail, Bassaris... more We characterized 15 polymorphic tetranucleotide microsatellite markers for the ringtail, Bassariscus astutus. We tested these loci in 21 individuals captured in Arizona and Texas and found six to 19 alleles per locus. Observed and expected heterozygosities ranged from 0.381 to 1.000 and from 0.381 to 0.941, respectively. All loci were in Hardy-Weinberg equilibrium, and none were in linkage disequilibrium. These markers may be used to investigate population genetics and mating patterns in this species.

Research paper thumbnail of Landscape genetics of California mule deer ( Odocoileus hemionus ): the roles of ecological and historical factors in generating differentiation

Research paper thumbnail of A novel assessment of population structure and gene flow in grey wolf populations of the Northern Rocky Mountains of the United States

Research paper thumbnail of The genealogy and genetic viability of reintroduced Yellowstone grey wolves

Research paper thumbnail of Rapid influenza A detection and quantitation in birds using a one-step real-time reverse transcriptase PCR and High Resolution Melting

Journal of Virological Methods, 2011

Efficient influenza A viral surveillance of wild and domestic birds requires rapid viral detectio... more Efficient influenza A viral surveillance of wild and domestic birds requires rapid viral detection and quantitation of high and low quality samples. Current influenza A qPCR-based detection protocols specified by CDC, OIE and USDA utilize fluorogenic hydrolysis probe based real-time reverse transcription PCR (RRT-PCR) assays for detection and quantitation. The sequence diversity of this virus, even in the conserved matrix gene M1, makes primer and probe designs challenging. In this report it was determined that false RRT-PCR positives are possible with this method. This is particularly problematic when surveying non-cultured or inactivated avian tracheal and cloacal mucosal samples with low concentrations of virus and large proportions of background nucleic acids. This report presents a modification of a one-step RRT-PCR detection method for influenza A using SYBR green intercalating dye-based target amplification detection. High Resolution Melting (HRM), amplicon size quantitation and sequence verification is used to screen for non-target amplification (false positives). The resulting protocol has the sensitivity of hydrolysis probe methods, allows for flexible primer design and verification of target amplification, and provides high confidence in positive results. A multiplex subtype detection method using the RRT-PCR HRM assay is also demonstrated. Overall, this method is both time and cost effective while providing an extra measure of confidence in surveillance results through the implementation of target verification.