This paper describes software created to search for and analyze pairs of duplicate genes within a... more This paper describes software created to search for and analyze pairs of duplicate genes within a genome. The process is based on a program that uses aligned amino acid sequences to generate a corresponding alignment of the underlying nucleotide sequences and perform a codon by codon comparison of the nucleotides. Observed numbers of nucleotide substitutions can be used to make inferences about the ages of gene duplication events and the effects of natural selection acting on duplicate genes.
Gene duplication has generally been viewed as a necessary source of material for the origin of ev... more Gene duplication has generally been viewed as a necessary source of material for the origin of evolutionary novelties, but it is unclear how often gene duplicates arise and how frequently they evolve new functions. Observations from the genomic databases for several eukaryotic species suggest that duplicate genes arise at a very high rate, on average 0.01 per gene per million years. Most duplicated genes experience a brief period of relaxed selection early in their history, with a moderate fraction of them evolving in an effectively neutral manner during this period. However, the vast majority of gene duplicates are silenced within a few million years, with the few survivors subsequently experiencing strong purifying selection. Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species.
The Genetic Simulation Library (GSL) is a set of C++ programs and classes that can be used in ind... more The Genetic Simulation Library (GSL) is a set of C++ programs and classes that can be used in individualbased simulation models of plant and animal populations. The classes in this library build representations of genes for a wide variety of different types of organisms, from asexually reproducing single-cell organisms to chromosome-structured sexually reproducing species.
Proceedings of IEEE International Electron Devices Meeting, 1993
... The coupling between the accelerator tanks and the klystrons is made with an iris, which is d... more ... The coupling between the accelerator tanks and the klystrons is made with an iris, which is designed so that there is a good match at the design beam current. When 4 4 /.1.1 IEDM 93-141 m Page 2. 75 keV 7 MeV 20 MeV ... 459-413,1988. (7) BP Murin, A.€! Durkin, 0.Yu. ...
Proceedings of the 1999 Particle Accelerator Conference (Cat. No.99CH36366), 1999
The Spallation Neutron Source (SNS) being built at Oak Ridge National Lab (ORNL) in Tennessee req... more The Spallation Neutron Source (SNS) being built at Oak Ridge National Lab (ORNL) in Tennessee requires a linac with an output energy of 1 GeV and an average current during the pulse of approximately 18 mA (including the effects of chopping). The average beam power for the initial baseline is 1 MW (1 mA average at 1 GeV). The linac is followed by an accumulator ring and target/instrument facility [1]. The RF system for the 1 MW linac requires 52 each 805 MHz klystrons and 3 each 402.5 MHz klystrons. The 805 MHz klystrons are configured in pairs to drive one resonant structure. This uses the installed RF very efficiently and in addition is convenient for the upgrade to 4 MW which must be considered in the design. The RF must have the correct amplitude and phase in order to ensure complete acceleration along the linac and to minimize beam loss. Due to the configuration proposed for SNS, the LLRF controls must equalize each pair of klystrons to ensure proper operation. The high voltage system for the klystrons will be based on Insulated Gate Bipolar Transistor (IGBT) technology to provide the best possible operation at the least cost.
Whole-genome duplications (WGD; polyploidization) can have significant and lasting effects on a s... more Whole-genome duplications (WGD; polyploidization) can have significant and lasting effects on a species and its descendent lineages, and have played a role in the evolution of many lineages, including vertebrates. New gene duplicates provide substrates for the evolution of novel genes and gene functions, and differential loss of duplicate genes in subpopulations may lead to reproductive isolation and rapid speciation. The genomes of Paramecium aurelia species shows evidence of three past WGDs (Aury et al. 2006), and the most recent genome duplication shortly predates the rise of the P. aurelia species complex of 15 morphologically identical species. We are sequencing the genomes of all P. aureliaspecies and several out-group species, as well as generating RNA seq data, in order to follow the outcomes of WGD in each species. Our initial genomes indicate a complicated story of differential gene lost in lineages, a surprisingly high rate of gene conversion between paralogs, and fundamental differences in mutation spectrum. With the completion of two out-group species' genomes, P. caudatum and multimicronucleatum, we are developing a much better understanding of the genome structures that predated the P. aurelia WGD.
The rate at which new mutations arise in the genome is a key factor in the evolution and adaptati... more The rate at which new mutations arise in the genome is a key factor in the evolution and adaptation of species. Here we describe the rate and spectrum of spontaneous mutations for the fission yeast Schizosaccharomyces pombe, a key model organism with many similarities to higher eukaryotes. We undertook an ~1700 generation mutation accumulation (MA) experiment with a haploid S. pombe, generating 422 single-base substitutions and 119 indels across the 96 replicates. This equates to a base substitution mutation rate of 2.00 x 10(-10) mutations per site per generation, similar to that reported for the distantly related budding yeast Saccharomyces cerevisiae. However, these two yeast species differ dramatically in their spectrum of base substitutions, the types of indels (S. pombe is more prone to insertions), and the pattern of selection required to counteract a strong AT biased mutation rate. Overall, our results indicate that GC-biased gene conversion does not play a major role in sha...
Proceedings of the 1997 Particle Accelerator Conference (Cat. No.97CH36167), 1998
The National Spallation Neutron Source (NSNS) system has been proposed to dramatically improve th... more The National Spallation Neutron Source (NSNS) system has been proposed to dramatically improve the neutron capabilities for science applications in the US. The NSNS is a fast pulse neutron source that would consist of a 1000 MeV H-linac, an accumulator ring, a neutron target, and an experimental area. Although the NSNS is to be built at Oak Ridge, the design
Deinococcus bacteria are extremely resistant to radiation, oxidation, and desiccation. Resilience... more Deinococcus bacteria are extremely resistant to radiation, oxidation, and desiccation. Resilience to these factors has been suggested to be due to enhanced damage prevention and repair mechanisms, as well as highly efficient antioxidant protection systems. Here, using mutation-accumulation experiments we find that the GC-rich Deinococcus radiodurans has an overall background genomic mutation rate similar to that of E. coli, but differs in mutation spectrum, with the A/T to G/C mutation rate (based on a total count of 88 A:T→G:C transitions and 82 A:T→C:G transversions) per site per generation higher than that in the other direction (based on a total count of 157 G:C→A:T transitions and 33 G:C→T:A transversions). We propose that this unique spectrum is shaped mainly by the abundant uracil DNA glycosylases (UDG) reducing G:C→T:A transversions, adenine methylation elevating A:T→C:G transversions, and absence of cytosine methylation decreasing G:C→A:T transitions. As opposed to the >...
IGARSS 2001. Scanning the Present and Resolving the Future. Proceedings. IEEE 2001 International Geoscience and Remote Sensing Symposium (Cat. No.01CH37217), 2001
ABSTRACT The aim of this work is to develop a satellite-based coastal water quality monitoring ca... more ABSTRACT The aim of this work is to develop a satellite-based coastal water quality monitoring capacity to assist in management of key anthropogenic activities on the coastal zone (ie. nutrient-rich wastewater, industrial and urban discharges, river and estuarine outflows). This tool will be applicable for the monitoring of long term water quality trends over local to regional scales to provide data on natural variation and long term trends in anthropogenically induced impacts. The project aims to develop a fundamental management tool that will be geographically transferable around the State and Australian Coastal Zone and which will be able to provide information at local, regional and statewide spatial scales, as required for management
IGARSS 2001. Scanning the Present and Resolving the Future. Proceedings. IEEE 2001 International Geoscience and Remote Sensing Symposium (Cat. No.01CH37217), 2001
The relationships between inherent optical properties of ocean waters and the subsurface diffuse ... more The relationships between inherent optical properties of ocean waters and the subsurface diffuse reflectance (R-) have been explored by a number of workers over the years. It is well accepted that R- is related to the backscattering to absorption ratio bb/a (or sometimes bb/(a+bb)) through R=fbb/a. The factor f has been described by a number of people, with various relationships being suggested for predicting its value. Until the development of "fast" oceanic radiative transfer models such as HYDROLIGHT, most workers have employed Monte Carlo techniques. This work presents results based on Monte Carlo investigations as well as comparisons with HYDROLIGHT results
It is well established on theoretical grounds that the accumulation of mildly deleterious mutatio... more It is well established on theoretical grounds that the accumulation of mildly deleterious mutations in nonrecombining genomes is a major extinction risk in obligately asexual populations. Sexual populations can also incur mutational deterioration in genomic regions that experience little or no recombination, i.e., autosomal regions near centromeres, Y chromosomes, and organelle genomes. Our results suggest, for a wide array of genes (transfer RNAs, ribosomal RNAs, and proteins) in a diverse collection of species (animals, plants, and fungi), an almost universal increase in the fixation probabilities of mildly deleterious mutations arising in mitochondrial and chloroplast genomes relative to those arising in the recombining nuclear genome. This enhanced width of the selective sieve in organelle genomes does not appear to be a consequence of relaxed selection, but can be explained by the decline in the efficiency of selection that results from the reduction of effective population siz...
IEEE International Geoscience and Remote Sensing Symposium, 2002
Many multitemporal change detection studies require calibrated sequences of satellite imagery to ... more Many multitemporal change detection studies require calibrated sequences of satellite imagery to monitor changes in the Earth surface free of the affects of atmospheric and other influences. Two image calibration procedures were assessed for their ability to estimate the atmospheric contribution to the satellite signal from the calibration results. A sequence of TM and ETM+ imagery over Hay (93/84) was
Despite the general assumption that site-specific mutation rates are independent of the local seq... more Despite the general assumption that site-specific mutation rates are independent of the local sequence context, a growing body of evidence suggests otherwise. To further examine context-dependent patterns of mutation, we amassed 5645 spontaneous mutations in wild-type and mismatch-repair deficient mutation accumulation lines of the gram-positive model organism Bacillus subtilis. We then analysed > 7500 spontaneous base-substitution mutations across Bacillus subtilis, Escherichia coli, and Mesoplasma florum wild-type and mismatch-repair deficient mutation-accumulation lines, finding a context-dependent mutation pattern that is asymmetric around the origin of replication. Different neighbouring nucleotides can alter site-specific mutation rates by as much as 75-fold, with sites neighbouring G:C base pairs or dimers involving alternating pyrimidine-purine and purine-pyrimidine nucleotides having significantly elevated mutation rates. The influence of context-dependent mutation on ge...
This paper describes software created to search for and analyze pairs of duplicate genes within a... more This paper describes software created to search for and analyze pairs of duplicate genes within a genome. The process is based on a program that uses aligned amino acid sequences to generate a corresponding alignment of the underlying nucleotide sequences and perform a codon by codon comparison of the nucleotides. Observed numbers of nucleotide substitutions can be used to make inferences about the ages of gene duplication events and the effects of natural selection acting on duplicate genes.
Gene duplication has generally been viewed as a necessary source of material for the origin of ev... more Gene duplication has generally been viewed as a necessary source of material for the origin of evolutionary novelties, but it is unclear how often gene duplicates arise and how frequently they evolve new functions. Observations from the genomic databases for several eukaryotic species suggest that duplicate genes arise at a very high rate, on average 0.01 per gene per million years. Most duplicated genes experience a brief period of relaxed selection early in their history, with a moderate fraction of them evolving in an effectively neutral manner during this period. However, the vast majority of gene duplicates are silenced within a few million years, with the few survivors subsequently experiencing strong purifying selection. Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species.
The Genetic Simulation Library (GSL) is a set of C++ programs and classes that can be used in ind... more The Genetic Simulation Library (GSL) is a set of C++ programs and classes that can be used in individualbased simulation models of plant and animal populations. The classes in this library build representations of genes for a wide variety of different types of organisms, from asexually reproducing single-cell organisms to chromosome-structured sexually reproducing species.
Proceedings of IEEE International Electron Devices Meeting, 1993
... The coupling between the accelerator tanks and the klystrons is made with an iris, which is d... more ... The coupling between the accelerator tanks and the klystrons is made with an iris, which is designed so that there is a good match at the design beam current. When 4 4 /.1.1 IEDM 93-141 m Page 2. 75 keV 7 MeV 20 MeV ... 459-413,1988. (7) BP Murin, A.€! Durkin, 0.Yu. ...
Proceedings of the 1999 Particle Accelerator Conference (Cat. No.99CH36366), 1999
The Spallation Neutron Source (SNS) being built at Oak Ridge National Lab (ORNL) in Tennessee req... more The Spallation Neutron Source (SNS) being built at Oak Ridge National Lab (ORNL) in Tennessee requires a linac with an output energy of 1 GeV and an average current during the pulse of approximately 18 mA (including the effects of chopping). The average beam power for the initial baseline is 1 MW (1 mA average at 1 GeV). The linac is followed by an accumulator ring and target/instrument facility [1]. The RF system for the 1 MW linac requires 52 each 805 MHz klystrons and 3 each 402.5 MHz klystrons. The 805 MHz klystrons are configured in pairs to drive one resonant structure. This uses the installed RF very efficiently and in addition is convenient for the upgrade to 4 MW which must be considered in the design. The RF must have the correct amplitude and phase in order to ensure complete acceleration along the linac and to minimize beam loss. Due to the configuration proposed for SNS, the LLRF controls must equalize each pair of klystrons to ensure proper operation. The high voltage system for the klystrons will be based on Insulated Gate Bipolar Transistor (IGBT) technology to provide the best possible operation at the least cost.
Whole-genome duplications (WGD; polyploidization) can have significant and lasting effects on a s... more Whole-genome duplications (WGD; polyploidization) can have significant and lasting effects on a species and its descendent lineages, and have played a role in the evolution of many lineages, including vertebrates. New gene duplicates provide substrates for the evolution of novel genes and gene functions, and differential loss of duplicate genes in subpopulations may lead to reproductive isolation and rapid speciation. The genomes of Paramecium aurelia species shows evidence of three past WGDs (Aury et al. 2006), and the most recent genome duplication shortly predates the rise of the P. aurelia species complex of 15 morphologically identical species. We are sequencing the genomes of all P. aureliaspecies and several out-group species, as well as generating RNA seq data, in order to follow the outcomes of WGD in each species. Our initial genomes indicate a complicated story of differential gene lost in lineages, a surprisingly high rate of gene conversion between paralogs, and fundamental differences in mutation spectrum. With the completion of two out-group species' genomes, P. caudatum and multimicronucleatum, we are developing a much better understanding of the genome structures that predated the P. aurelia WGD.
The rate at which new mutations arise in the genome is a key factor in the evolution and adaptati... more The rate at which new mutations arise in the genome is a key factor in the evolution and adaptation of species. Here we describe the rate and spectrum of spontaneous mutations for the fission yeast Schizosaccharomyces pombe, a key model organism with many similarities to higher eukaryotes. We undertook an ~1700 generation mutation accumulation (MA) experiment with a haploid S. pombe, generating 422 single-base substitutions and 119 indels across the 96 replicates. This equates to a base substitution mutation rate of 2.00 x 10(-10) mutations per site per generation, similar to that reported for the distantly related budding yeast Saccharomyces cerevisiae. However, these two yeast species differ dramatically in their spectrum of base substitutions, the types of indels (S. pombe is more prone to insertions), and the pattern of selection required to counteract a strong AT biased mutation rate. Overall, our results indicate that GC-biased gene conversion does not play a major role in sha...
Proceedings of the 1997 Particle Accelerator Conference (Cat. No.97CH36167), 1998
The National Spallation Neutron Source (NSNS) system has been proposed to dramatically improve th... more The National Spallation Neutron Source (NSNS) system has been proposed to dramatically improve the neutron capabilities for science applications in the US. The NSNS is a fast pulse neutron source that would consist of a 1000 MeV H-linac, an accumulator ring, a neutron target, and an experimental area. Although the NSNS is to be built at Oak Ridge, the design
Deinococcus bacteria are extremely resistant to radiation, oxidation, and desiccation. Resilience... more Deinococcus bacteria are extremely resistant to radiation, oxidation, and desiccation. Resilience to these factors has been suggested to be due to enhanced damage prevention and repair mechanisms, as well as highly efficient antioxidant protection systems. Here, using mutation-accumulation experiments we find that the GC-rich Deinococcus radiodurans has an overall background genomic mutation rate similar to that of E. coli, but differs in mutation spectrum, with the A/T to G/C mutation rate (based on a total count of 88 A:T→G:C transitions and 82 A:T→C:G transversions) per site per generation higher than that in the other direction (based on a total count of 157 G:C→A:T transitions and 33 G:C→T:A transversions). We propose that this unique spectrum is shaped mainly by the abundant uracil DNA glycosylases (UDG) reducing G:C→T:A transversions, adenine methylation elevating A:T→C:G transversions, and absence of cytosine methylation decreasing G:C→A:T transitions. As opposed to the >...
IGARSS 2001. Scanning the Present and Resolving the Future. Proceedings. IEEE 2001 International Geoscience and Remote Sensing Symposium (Cat. No.01CH37217), 2001
ABSTRACT The aim of this work is to develop a satellite-based coastal water quality monitoring ca... more ABSTRACT The aim of this work is to develop a satellite-based coastal water quality monitoring capacity to assist in management of key anthropogenic activities on the coastal zone (ie. nutrient-rich wastewater, industrial and urban discharges, river and estuarine outflows). This tool will be applicable for the monitoring of long term water quality trends over local to regional scales to provide data on natural variation and long term trends in anthropogenically induced impacts. The project aims to develop a fundamental management tool that will be geographically transferable around the State and Australian Coastal Zone and which will be able to provide information at local, regional and statewide spatial scales, as required for management
IGARSS 2001. Scanning the Present and Resolving the Future. Proceedings. IEEE 2001 International Geoscience and Remote Sensing Symposium (Cat. No.01CH37217), 2001
The relationships between inherent optical properties of ocean waters and the subsurface diffuse ... more The relationships between inherent optical properties of ocean waters and the subsurface diffuse reflectance (R-) have been explored by a number of workers over the years. It is well accepted that R- is related to the backscattering to absorption ratio bb/a (or sometimes bb/(a+bb)) through R=fbb/a. The factor f has been described by a number of people, with various relationships being suggested for predicting its value. Until the development of "fast" oceanic radiative transfer models such as HYDROLIGHT, most workers have employed Monte Carlo techniques. This work presents results based on Monte Carlo investigations as well as comparisons with HYDROLIGHT results
It is well established on theoretical grounds that the accumulation of mildly deleterious mutatio... more It is well established on theoretical grounds that the accumulation of mildly deleterious mutations in nonrecombining genomes is a major extinction risk in obligately asexual populations. Sexual populations can also incur mutational deterioration in genomic regions that experience little or no recombination, i.e., autosomal regions near centromeres, Y chromosomes, and organelle genomes. Our results suggest, for a wide array of genes (transfer RNAs, ribosomal RNAs, and proteins) in a diverse collection of species (animals, plants, and fungi), an almost universal increase in the fixation probabilities of mildly deleterious mutations arising in mitochondrial and chloroplast genomes relative to those arising in the recombining nuclear genome. This enhanced width of the selective sieve in organelle genomes does not appear to be a consequence of relaxed selection, but can be explained by the decline in the efficiency of selection that results from the reduction of effective population siz...
IEEE International Geoscience and Remote Sensing Symposium, 2002
Many multitemporal change detection studies require calibrated sequences of satellite imagery to ... more Many multitemporal change detection studies require calibrated sequences of satellite imagery to monitor changes in the Earth surface free of the affects of atmospheric and other influences. Two image calibration procedures were assessed for their ability to estimate the atmospheric contribution to the satellite signal from the calibration results. A sequence of TM and ETM+ imagery over Hay (93/84) was
Despite the general assumption that site-specific mutation rates are independent of the local seq... more Despite the general assumption that site-specific mutation rates are independent of the local sequence context, a growing body of evidence suggests otherwise. To further examine context-dependent patterns of mutation, we amassed 5645 spontaneous mutations in wild-type and mismatch-repair deficient mutation accumulation lines of the gram-positive model organism Bacillus subtilis. We then analysed > 7500 spontaneous base-substitution mutations across Bacillus subtilis, Escherichia coli, and Mesoplasma florum wild-type and mismatch-repair deficient mutation-accumulation lines, finding a context-dependent mutation pattern that is asymmetric around the origin of replication. Different neighbouring nucleotides can alter site-specific mutation rates by as much as 75-fold, with sites neighbouring G:C base pairs or dimers involving alternating pyrimidine-purine and purine-pyrimidine nucleotides having significantly elevated mutation rates. The influence of context-dependent mutation on ge...
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Papers by Clodagh Lynch