Abstract We have designed and built electrostatically actuated microvalves compatible with integr... more Abstract We have designed and built electrostatically actuated microvalves compatible with integration into a PDMS based microfluidic system. The key innovation for electrostatic actuation was the incorporation of carbon nanotubes into the PDMS valve membrane, ...
Two international workshops have been held that focused on the production modeling approach, at v... more Two international workshops have been held that focused on the production modeling approach, at various levels of aggregation and with various covariates. How the outputs from such models could be used to estimate management-relevant metrics and ecosystem attributes was examined. The objectives were to A) use comparative analyses to build a methodological foundation for evaluating how ecosystem structure and function interact to support fisheries production, B) determine what processes control spatial and temporal variation in ecosystem services, and C) use surplus production modeling as a unifying tool to evaluate the relative effects of physical forcing, trophodynamics, and fisheries exploitation on fish production. To support these objectives, a database was created which incorporated biomass and landings data for 97 commercially and ecologically important fish and invertebrate species in 11 different Canadian, US, and Norwegian large marine ecosystems. Climate data were also inc...
Multiple drivers of productivity in fishery ecosystems simultaneously interact to determine overa... more Multiple drivers of productivity in fishery ecosystems simultaneously interact to determine overall production levels. These drivers reflect the triad of factors influencing fisheries production including fisheries, the environment, and trophodynamics. Teasing apart the copious processes that dampen, amplify, modulate or enhance fisheries production requires a concurrent examination of a suite of indicators; a comparative approach to ecosystems also has merit in elucidating the relative dynamics of these processes. Here we briefly describe and present a suite of biological indicators, loosely centered around fisheries production, as derived from standard fisheries independent and dependent surveys for 11 northern hemisphere ecosystems. We also describe and present indicators that capture important fisheries drivers, environmental drivers, and trophodynamic drivers. These represent common indicators that are beginning to be adopted more broadly in an international context. More germa...
Abstract We have designed and built electrostatically actuated microvalves compatible with integr... more Abstract We have designed and built electrostatically actuated microvalves compatible with integration into a PDMS based microfluidic system. The key innovation for electrostatic actuation was the incorporation of carbon nanotubes into the PDMS valve membrane, ...
Prepared by Sandia National Laboratories Albuquerque, New Mexico 87185 and Livermore, California ... more Prepared by Sandia National Laboratories Albuquerque, New Mexico 87185 and Livermore, California 94550 Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security ...
Affinity maturation and class switching of antibodies requires activation-induced cytidine deamin... more Affinity maturation and class switching of antibodies requires activation-induced cytidine deaminase (AID)-dependent hypermutation of Ig V(D)J rearrangements and Ig S regions, respectively, in activated B cells. AID deaminates deoxycytidine bases in Ig genes, converting them into deoxyuridines. In V(D)J regions, subsequent excision of the deaminated bases by uracil-DNA glycosylase, or by mismatch repair, leads to further point mutation or gene conversion, depending on the species. In Ig S regions, nicking at the abasic sites produced by AID and uracil-DNA glycosylases results in staggered double-strand breaks, whose repair by nonhomologous end joining mediates Ig class switching. We have tested whether nonhomologous end joining also plays a role in V(D)J hypermutation using chicken DT40 cells deficient for Ku70 or the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). Inactivation of the Ku70 or DNA-PKcs genes in DT40 cells elevated the rate of AID-induced gene conversion as much as 5-fold. Furthermore, DNA-PKcs-deficiency appeared to reduce point mutation. The data provide strong evidence that doublestrand DNA ends capable of recruiting the DNA-dependent protein kinase complex are important intermediates in Ig V gene conversion. Citation: Cook AJL, Raftery JM, Lau KKE, Jessup A, Harris RS, et al. (2007) DNA-dependent protein kinase inhibits AID-induced antibody gene conversion. PLoS Biol 5(4): e80.
Marine ecosystems are influenced by drivers that operate and interact over multiple scales, resul... more Marine ecosystems are influenced by drivers that operate and interact over multiple scales, resulting in nonlinear or abrupt responses to perturbation. Because of the inherent complexity of marine ecosystems, progress towards an understanding of factors that affect fisheries production will be most efficient if researchers adopt a comparative approach across ecosystems using suites of indicators. The goals of this study were to explore a suite of biomass-and catchbased ecosystem response indicators for 9 northern hemisphere ecosystems relative to indices that capture the influence of fisheries, trophodynamic and environmental drivers, and to compare the relative influence of the triad of drivers. Partial least squares regression was used to explore relationships between the ecosystem response indicators and predictor drivers and to estimate the relative importance of each of the triad of drivers. Across ecosystems we have identified a few common observations: (1) environmental drivers, particularly temperature-related independent variables, are most likely related to total system biomass and biomass of specific biological groups (e.g. gadoid or clupeid fishes); (2) trophodynamic drivers are most relevant to the mean trophic level of community and the demersal-to-pelagic biomass ratio; and (3) fisheries drivers tend to be related to the catch-based indicators, such as fishing-in-balance and percent of primary production required to support fisheries. Overall, each of the triad of drivers was important for all ecosystems; however, the relative importance of each driver and the indicators they most affected varied among ecosystems, suggesting that an examination of a suite of indicators and drivers is required. A key finding is that fishing is categorically an important driver, but to explain biomass trends it is very important to consider environmental drivers as well.
Metrics representative of key ecosystem processes are required for monitoring and understanding s... more Metrics representative of key ecosystem processes are required for monitoring and understanding system dynamics, as a function of ecosystem-based fisheries management (EBFM).
Interbreeding between artificially-selected and wild organisms can have negative fitness conseque... more Interbreeding between artificially-selected and wild organisms can have negative fitness consequences for the latter. In the Northwest Atlantic, farmed Atlantic salmon recurrently escape into the wild and enter rivers where small, declining populations of wild salmon breed. Most farmed salmon in the region derive from an ancestral source population that occupies a nonacidified river (pH 6.0-6.5). Yet many wild populations with which escaped farmed salmon might interbreed inhabit acidified rivers (pH 4.6-5.2). Using common garden experimentation, and examining two early-life history stages across two generations of interbreeding, we showed that wild salmon populations inhabiting acidified rivers had higher survival at acidified pH than farmed salmon or F 1 farmedwild hybrids. In contrast, however, there was limited evidence for reduced performance in backcrosses, and F 2 farmed-wild hybrids performed better or equally well to wild salmon. Wild salmon also survived or grew better at nonacidified than acidified pH, and wild and farmed salmon survived equally well at nonacidified pH. Thus, for acid tolerance and the stages examined, we found some evidence both for and against the theory that repeated farmed-wild interbreeding may reduce adaptive genetic variation in the wild and thereby negatively affect the persistence of depleted wild populations.
Abstract We have designed and built electrostatically actuated microvalves compatible with integr... more Abstract We have designed and built electrostatically actuated microvalves compatible with integration into a PDMS based microfluidic system. The key innovation for electrostatic actuation was the incorporation of carbon nanotubes into the PDMS valve membrane, ...
Two international workshops have been held that focused on the production modeling approach, at v... more Two international workshops have been held that focused on the production modeling approach, at various levels of aggregation and with various covariates. How the outputs from such models could be used to estimate management-relevant metrics and ecosystem attributes was examined. The objectives were to A) use comparative analyses to build a methodological foundation for evaluating how ecosystem structure and function interact to support fisheries production, B) determine what processes control spatial and temporal variation in ecosystem services, and C) use surplus production modeling as a unifying tool to evaluate the relative effects of physical forcing, trophodynamics, and fisheries exploitation on fish production. To support these objectives, a database was created which incorporated biomass and landings data for 97 commercially and ecologically important fish and invertebrate species in 11 different Canadian, US, and Norwegian large marine ecosystems. Climate data were also inc...
Multiple drivers of productivity in fishery ecosystems simultaneously interact to determine overa... more Multiple drivers of productivity in fishery ecosystems simultaneously interact to determine overall production levels. These drivers reflect the triad of factors influencing fisheries production including fisheries, the environment, and trophodynamics. Teasing apart the copious processes that dampen, amplify, modulate or enhance fisheries production requires a concurrent examination of a suite of indicators; a comparative approach to ecosystems also has merit in elucidating the relative dynamics of these processes. Here we briefly describe and present a suite of biological indicators, loosely centered around fisheries production, as derived from standard fisheries independent and dependent surveys for 11 northern hemisphere ecosystems. We also describe and present indicators that capture important fisheries drivers, environmental drivers, and trophodynamic drivers. These represent common indicators that are beginning to be adopted more broadly in an international context. More germa...
Abstract We have designed and built electrostatically actuated microvalves compatible with integr... more Abstract We have designed and built electrostatically actuated microvalves compatible with integration into a PDMS based microfluidic system. The key innovation for electrostatic actuation was the incorporation of carbon nanotubes into the PDMS valve membrane, ...
Prepared by Sandia National Laboratories Albuquerque, New Mexico 87185 and Livermore, California ... more Prepared by Sandia National Laboratories Albuquerque, New Mexico 87185 and Livermore, California 94550 Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security ...
Affinity maturation and class switching of antibodies requires activation-induced cytidine deamin... more Affinity maturation and class switching of antibodies requires activation-induced cytidine deaminase (AID)-dependent hypermutation of Ig V(D)J rearrangements and Ig S regions, respectively, in activated B cells. AID deaminates deoxycytidine bases in Ig genes, converting them into deoxyuridines. In V(D)J regions, subsequent excision of the deaminated bases by uracil-DNA glycosylase, or by mismatch repair, leads to further point mutation or gene conversion, depending on the species. In Ig S regions, nicking at the abasic sites produced by AID and uracil-DNA glycosylases results in staggered double-strand breaks, whose repair by nonhomologous end joining mediates Ig class switching. We have tested whether nonhomologous end joining also plays a role in V(D)J hypermutation using chicken DT40 cells deficient for Ku70 or the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). Inactivation of the Ku70 or DNA-PKcs genes in DT40 cells elevated the rate of AID-induced gene conversion as much as 5-fold. Furthermore, DNA-PKcs-deficiency appeared to reduce point mutation. The data provide strong evidence that doublestrand DNA ends capable of recruiting the DNA-dependent protein kinase complex are important intermediates in Ig V gene conversion. Citation: Cook AJL, Raftery JM, Lau KKE, Jessup A, Harris RS, et al. (2007) DNA-dependent protein kinase inhibits AID-induced antibody gene conversion. PLoS Biol 5(4): e80.
Marine ecosystems are influenced by drivers that operate and interact over multiple scales, resul... more Marine ecosystems are influenced by drivers that operate and interact over multiple scales, resulting in nonlinear or abrupt responses to perturbation. Because of the inherent complexity of marine ecosystems, progress towards an understanding of factors that affect fisheries production will be most efficient if researchers adopt a comparative approach across ecosystems using suites of indicators. The goals of this study were to explore a suite of biomass-and catchbased ecosystem response indicators for 9 northern hemisphere ecosystems relative to indices that capture the influence of fisheries, trophodynamic and environmental drivers, and to compare the relative influence of the triad of drivers. Partial least squares regression was used to explore relationships between the ecosystem response indicators and predictor drivers and to estimate the relative importance of each of the triad of drivers. Across ecosystems we have identified a few common observations: (1) environmental drivers, particularly temperature-related independent variables, are most likely related to total system biomass and biomass of specific biological groups (e.g. gadoid or clupeid fishes); (2) trophodynamic drivers are most relevant to the mean trophic level of community and the demersal-to-pelagic biomass ratio; and (3) fisheries drivers tend to be related to the catch-based indicators, such as fishing-in-balance and percent of primary production required to support fisheries. Overall, each of the triad of drivers was important for all ecosystems; however, the relative importance of each driver and the indicators they most affected varied among ecosystems, suggesting that an examination of a suite of indicators and drivers is required. A key finding is that fishing is categorically an important driver, but to explain biomass trends it is very important to consider environmental drivers as well.
Metrics representative of key ecosystem processes are required for monitoring and understanding s... more Metrics representative of key ecosystem processes are required for monitoring and understanding system dynamics, as a function of ecosystem-based fisheries management (EBFM).
Interbreeding between artificially-selected and wild organisms can have negative fitness conseque... more Interbreeding between artificially-selected and wild organisms can have negative fitness consequences for the latter. In the Northwest Atlantic, farmed Atlantic salmon recurrently escape into the wild and enter rivers where small, declining populations of wild salmon breed. Most farmed salmon in the region derive from an ancestral source population that occupies a nonacidified river (pH 6.0-6.5). Yet many wild populations with which escaped farmed salmon might interbreed inhabit acidified rivers (pH 4.6-5.2). Using common garden experimentation, and examining two early-life history stages across two generations of interbreeding, we showed that wild salmon populations inhabiting acidified rivers had higher survival at acidified pH than farmed salmon or F 1 farmedwild hybrids. In contrast, however, there was limited evidence for reduced performance in backcrosses, and F 2 farmed-wild hybrids performed better or equally well to wild salmon. Wild salmon also survived or grew better at nonacidified than acidified pH, and wild and farmed salmon survived equally well at nonacidified pH. Thus, for acid tolerance and the stages examined, we found some evidence both for and against the theory that repeated farmed-wild interbreeding may reduce adaptive genetic variation in the wild and thereby negatively affect the persistence of depleted wild populations.
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