Autophagy, an intracellular recycling system, is essential for the meiotic maturation of porcine ... more Autophagy, an intracellular recycling system, is essential for the meiotic maturation of porcine oocytes. Trehalose has been reported as a novel mammalian target of rapamycin (mTOR)-independent autophagy inducer in many cells. Furthermore, we previously have demonstrated that trehalose supplementation during in vitro maturation of porcine oocytes improves the developmental competence of parthenogenetic embryos, possibly via autophagic activation, whereas the underlying mechanisms remain unclear. Therefore, the aim of this study was to address this issue. We found that trehalose plays a role as an autophagy activator by autophagic flux assay and determined that it promotes phosphatidylinositol-3 kinase (PI3K)/protein kinase B (Akt) inhibition and vacuolar protein sorting 34 (VPS34)/mTOR activation by immunoblotting, both in cumulus cells (CCs) and oocytes. However, interestingly, the effects and the mechanisms regulated by trehalose were different in them, respectively. In CCs, the autophagy was activated through the improvement of lysosomal function/autophagic clearance viability by upregulation of coordinated lysosomal expression and regulation genes via PI3K/Akt inhibition. Whereas in oocytes, autophagy was activated via induction of VPS34, which directly influences autophagosome formation, and the precise meiotic process was ensured via Akt inhibition and mTOR activation. Taken together, this study furtherly elucidates the novel detailed mechanism of trehalose during porcine oocyte maturation, thus laying the biological foundations for pharmacological application.
Canadian Journal of Fisheries and Aquatic Sciences, May 1, 2018
State-space models explicitly separate uncertainty associated with unobserved, time-varying param... more State-space models explicitly separate uncertainty associated with unobserved, time-varying parameters from that which arises from sampling the population. The statistical aspects of formal state-space models are appealing and these models are becoming more widely used for assessments. However, treating natural mortality as known and constant across ages continues to be common practice. We developed a state-space, age-structured assessment model that allowed different assumptions for natural mortality and the degree of temporal stochasticity in abundance. We fit a suite of models where natural mortality was either age-invariant or an allometric function of mass and interannual transitions of abundance were deterministic or stochastic to observations on Gulf of Maine – Georges Bank Acadian redfish (Sebastes fasciatus). We found that allowing stochasticity in the interannual transition in abundance was important and estimating age-invariant natural mortality was sufficient. A simulation study showed low bias in annual biomass estimation when the estimation and simulation model matched and the Akaike imformation criterion accurately measured relative model performance, but it was important to allow simulated data sets to include the stochasticity in interannual transitions of abundance-at-age.
Canadian Journal of Fisheries and Aquatic Sciences, Jul 1, 2005
We developed a model for in-season age-specific forecasts of salmon returns using preseason retur... more We developed a model for in-season age-specific forecasts of salmon returns using preseason return forecasts, age composition of in-season returns, cumulative in-season returns by fishing district, and age composition and an index of abundance from an in-season test fishery. We apply this method to the sockeye salmon (Oncorhynchus nerka) fishery in the Bristol Bay districts of Alaska. The model generates point estimates and Bayesian probability distributions for return numbers by age and river, and it provides an integrated framework for including all of the major data sources currently used in in-season forecasting. We evaluated model performance using early-season data from 19992001 and compared the effects of four information sets on forecast accuracy. The four information sets were as follows: I, district-specific inshore return data; II, inshore return data and test fishery data; III, inshore return data and preseason forecasts; IV, inshore return data, test fishery data, and preseason forecasts. Forecasts from information sets II, III, and IV were less biased than those from information set I. However, in terms of the forecast interval, forecasts from information set II were best because the 95% highest posterior density regions of forecasts from information set II covered the actual returns most frequently.
Transactions of The American Fisheries Society, Mar 1, 2012
The biological reference point Fx% (i.e., the fishing mortality rate that maintains the spawning ... more The biological reference point Fx% (i.e., the fishing mortality rate that maintains the spawning stock biomass per recruit at x% of its unfished value [where x is usually set to 40]) is a commonly used proxy for FMSY (the fishing mortality rate that results in the maximum sustainable yield). However, Fx% is not in general equivalent to FMSY. To investigate the difference between Fx% and FMSY, we developed a simple simulation model capable of representing the relationship between yield and fishing mortality, maximum spawning potential (%MSP), and the curvature of the stock–recruitment (S–R) curve (parameterized as β) for a stock similar to summer flounder Paralichthys dentatus (a high‐β species). The model demonstrates that the dynamic trajectories of the stock are heavily dependent on β. The model confirmed the dependence of equilibrium yield on β and produced a specific relationship between the magnitude of β and yield. A decision‐theoretic approach was used to suggest that setting x to 40 reduces yield and that smaller values of x produce greater yields for high‐β stocks. The analysis focuses attention on the fact that the choice of Fx% as a management tool places extreme reliance on the least known and understood component of fish population dynamics: the S–R relationship. Our conclusion (to use a value of x considerably less than 40 to obtain MSY) was supported by (1) our simulation results, (2) averaging in a decision‐theoretic approach, (3) the correspondence of the traditionally computed biomass at the maximum sustainable yield with high values of β, and (4) the values of x reported in the literature.
144th Annual Meeting of the American Fisheries Society, Aug 21, 2014
ABSTRACT Fishermen reported that Georges Bank yellowtail flounder (Limanda ferruginea) migrated t... more ABSTRACT Fishermen reported that Georges Bank yellowtail flounder (Limanda ferruginea) migrated to deeper waters during 2000–2004 and 2006–2010. To test this hypothesis, we analyzed fishery data from otter trawl vessels targeting a mixed groundfish complex over the 10 year period, using a statistical linear model with catch-per-unit-effort weighted depth as the response variable, and abiotic (e.g., bottom water temperature) and biotic (e.g., skate and dogfish catch) data as predictor variables. We considered mixed as well as fixed effect models to account for dependence or correlation in catches among hauls within a trip. Yellowtail flounder shifted to deeper waters during the 10 years. Bottom water temperature had a greater influence on the movement than the distribution of skate or dogfish. Optimal water temperature was about 6.8 °C from the fixed effect model and about 7.1 °C from the mixed effect model. Skate distribution affected yellowtail flounder depth more than dogfish distribution. The mixed effect model was more parsimonious than the fixed effect model, although the latter fitted the data better and performed better under cross validation.
Transactions of The American Fisheries Society, 2012
Unless accounted for in the estimation, tag loss will cause mark–recapture methods to overestimat... more Unless accounted for in the estimation, tag loss will cause mark–recapture methods to overestimate the true abundance of a closed population and to underestimate the associated uncertainty. Current methods of accounting for tag loss require all marked individuals to be double‐tagged. We present a new model that fully accounts for tag loss and allows for the use of a mixture of single‐ and double‐tagged individuals, thus simplifying implementation in the field. Treating abundance, tag loss rate, and capture probabilities as free parameters, we estimated those parameters and their uncertainty by using maximum likelihood. Whereas existing methods assume that a double‐tagged animal does not lose both tags, the new model allows the animal to lose both tags. The new model's performance was assessed and compared with that of other estimators (modified Petersen and Seber–Felton) via simulation. As expected, estimates from the new model were less biased and more precise than estimates from the other models. The model was used to estimate the abundance of the kokanee Oncorhynchus nerka population in the Metolius River, Oregon, during 2007. Abundance was estimated at 102,970 fish (), tag loss rate was estimated at 0.27 (), the capture probability for the first sample (tagging) was 0.03 (), and the capture probability for the second sample (recovery) was 0.11 (). The new model uses all of the information from single‐ and double‐tag data, provides unbiased abundance estimates in the presence of tag loss for a closed population, and has less‐stringent field requirements that make it easier to employ than other methods.
Autophagy, an intracellular recycling system, is essential for the meiotic maturation of porcine ... more Autophagy, an intracellular recycling system, is essential for the meiotic maturation of porcine oocytes. Trehalose has been reported as a novel mammalian target of rapamycin (mTOR)-independent autophagy inducer in many cells. Furthermore, we previously have demonstrated that trehalose supplementation during in vitro maturation of porcine oocytes improves the developmental competence of parthenogenetic embryos, possibly via autophagic activation, whereas the underlying mechanisms remain unclear. Therefore, the aim of this study was to address this issue. We found that trehalose plays a role as an autophagy activator by autophagic flux assay and determined that it promotes phosphatidylinositol-3 kinase (PI3K)/protein kinase B (Akt) inhibition and vacuolar protein sorting 34 (VPS34)/mTOR activation by immunoblotting, both in cumulus cells (CCs) and oocytes. However, interestingly, the effects and the mechanisms regulated by trehalose were different in them, respectively. In CCs, the autophagy was activated through the improvement of lysosomal function/autophagic clearance viability by upregulation of coordinated lysosomal expression and regulation genes via PI3K/Akt inhibition. Whereas in oocytes, autophagy was activated via induction of VPS34, which directly influences autophagosome formation, and the precise meiotic process was ensured via Akt inhibition and mTOR activation. Taken together, this study furtherly elucidates the novel detailed mechanism of trehalose during porcine oocyte maturation, thus laying the biological foundations for pharmacological application.
Canadian Journal of Fisheries and Aquatic Sciences, May 1, 2018
State-space models explicitly separate uncertainty associated with unobserved, time-varying param... more State-space models explicitly separate uncertainty associated with unobserved, time-varying parameters from that which arises from sampling the population. The statistical aspects of formal state-space models are appealing and these models are becoming more widely used for assessments. However, treating natural mortality as known and constant across ages continues to be common practice. We developed a state-space, age-structured assessment model that allowed different assumptions for natural mortality and the degree of temporal stochasticity in abundance. We fit a suite of models where natural mortality was either age-invariant or an allometric function of mass and interannual transitions of abundance were deterministic or stochastic to observations on Gulf of Maine – Georges Bank Acadian redfish (Sebastes fasciatus). We found that allowing stochasticity in the interannual transition in abundance was important and estimating age-invariant natural mortality was sufficient. A simulation study showed low bias in annual biomass estimation when the estimation and simulation model matched and the Akaike imformation criterion accurately measured relative model performance, but it was important to allow simulated data sets to include the stochasticity in interannual transitions of abundance-at-age.
Canadian Journal of Fisheries and Aquatic Sciences, Jul 1, 2005
We developed a model for in-season age-specific forecasts of salmon returns using preseason retur... more We developed a model for in-season age-specific forecasts of salmon returns using preseason return forecasts, age composition of in-season returns, cumulative in-season returns by fishing district, and age composition and an index of abundance from an in-season test fishery. We apply this method to the sockeye salmon (Oncorhynchus nerka) fishery in the Bristol Bay districts of Alaska. The model generates point estimates and Bayesian probability distributions for return numbers by age and river, and it provides an integrated framework for including all of the major data sources currently used in in-season forecasting. We evaluated model performance using early-season data from 19992001 and compared the effects of four information sets on forecast accuracy. The four information sets were as follows: I, district-specific inshore return data; II, inshore return data and test fishery data; III, inshore return data and preseason forecasts; IV, inshore return data, test fishery data, and preseason forecasts. Forecasts from information sets II, III, and IV were less biased than those from information set I. However, in terms of the forecast interval, forecasts from information set II were best because the 95% highest posterior density regions of forecasts from information set II covered the actual returns most frequently.
Transactions of The American Fisheries Society, Mar 1, 2012
The biological reference point Fx% (i.e., the fishing mortality rate that maintains the spawning ... more The biological reference point Fx% (i.e., the fishing mortality rate that maintains the spawning stock biomass per recruit at x% of its unfished value [where x is usually set to 40]) is a commonly used proxy for FMSY (the fishing mortality rate that results in the maximum sustainable yield). However, Fx% is not in general equivalent to FMSY. To investigate the difference between Fx% and FMSY, we developed a simple simulation model capable of representing the relationship between yield and fishing mortality, maximum spawning potential (%MSP), and the curvature of the stock–recruitment (S–R) curve (parameterized as β) for a stock similar to summer flounder Paralichthys dentatus (a high‐β species). The model demonstrates that the dynamic trajectories of the stock are heavily dependent on β. The model confirmed the dependence of equilibrium yield on β and produced a specific relationship between the magnitude of β and yield. A decision‐theoretic approach was used to suggest that setting x to 40 reduces yield and that smaller values of x produce greater yields for high‐β stocks. The analysis focuses attention on the fact that the choice of Fx% as a management tool places extreme reliance on the least known and understood component of fish population dynamics: the S–R relationship. Our conclusion (to use a value of x considerably less than 40 to obtain MSY) was supported by (1) our simulation results, (2) averaging in a decision‐theoretic approach, (3) the correspondence of the traditionally computed biomass at the maximum sustainable yield with high values of β, and (4) the values of x reported in the literature.
144th Annual Meeting of the American Fisheries Society, Aug 21, 2014
ABSTRACT Fishermen reported that Georges Bank yellowtail flounder (Limanda ferruginea) migrated t... more ABSTRACT Fishermen reported that Georges Bank yellowtail flounder (Limanda ferruginea) migrated to deeper waters during 2000–2004 and 2006–2010. To test this hypothesis, we analyzed fishery data from otter trawl vessels targeting a mixed groundfish complex over the 10 year period, using a statistical linear model with catch-per-unit-effort weighted depth as the response variable, and abiotic (e.g., bottom water temperature) and biotic (e.g., skate and dogfish catch) data as predictor variables. We considered mixed as well as fixed effect models to account for dependence or correlation in catches among hauls within a trip. Yellowtail flounder shifted to deeper waters during the 10 years. Bottom water temperature had a greater influence on the movement than the distribution of skate or dogfish. Optimal water temperature was about 6.8 °C from the fixed effect model and about 7.1 °C from the mixed effect model. Skate distribution affected yellowtail flounder depth more than dogfish distribution. The mixed effect model was more parsimonious than the fixed effect model, although the latter fitted the data better and performed better under cross validation.
Transactions of The American Fisheries Society, 2012
Unless accounted for in the estimation, tag loss will cause mark–recapture methods to overestimat... more Unless accounted for in the estimation, tag loss will cause mark–recapture methods to overestimate the true abundance of a closed population and to underestimate the associated uncertainty. Current methods of accounting for tag loss require all marked individuals to be double‐tagged. We present a new model that fully accounts for tag loss and allows for the use of a mixture of single‐ and double‐tagged individuals, thus simplifying implementation in the field. Treating abundance, tag loss rate, and capture probabilities as free parameters, we estimated those parameters and their uncertainty by using maximum likelihood. Whereas existing methods assume that a double‐tagged animal does not lose both tags, the new model allows the animal to lose both tags. The new model's performance was assessed and compared with that of other estimators (modified Petersen and Seber–Felton) via simulation. As expected, estimates from the new model were less biased and more precise than estimates from the other models. The model was used to estimate the abundance of the kokanee Oncorhynchus nerka population in the Metolius River, Oregon, during 2007. Abundance was estimated at 102,970 fish (), tag loss rate was estimated at 0.27 (), the capture probability for the first sample (tagging) was 0.03 (), and the capture probability for the second sample (recovery) was 0.11 (). The new model uses all of the information from single‐ and double‐tag data, provides unbiased abundance estimates in the presence of tag loss for a closed population, and has less‐stringent field requirements that make it easier to employ than other methods.
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Papers by Saang-Yoon Hyun