Comparison of habitat-based indices of abundance with fishery-independent biomass estimates from bottom trawl surveys

Rockfish species are notoriously difficult to sample with multispecies bottom trawl survey methods. Typically, biomass estimates have high coefficients of variation and can fluctuate outside the bounds of biological reality from year to year. This variation may be due in part to their patchy distribution related to very specific habitat preferences. We successfully modeled the distribution of five commercially important and abundant rockf ish species. A two-stage modeling method (modeling both presence-absence and abundance) and a collection of important habitat variables were used to predict bottom trawl survey catch per unit of effort. The resulting models explained between 22% and 66% of the variation in rockfish distribution. The models were largely driven by depth, local slope, bottom temperature, abundance of coral and sponge, and measures of water column productivity (i.e., phytoplankton and zooplankton). A year-effect in the models was back-transformed and used as an index of the time series of abundance. The abundance index trajectories of three of five species were similar to the existing estimates of their biomass. In the majority of cases the habitat-based indices exhibited less interannual variability and similar precision when compared with stratified survey-based biomass estimates. These indices may provide for stock assessment models a more stable alternative to current biomass estimates produced by the multispecies bottom trawl survey in the Gulf of Alaska.

Effects of maternal age and size on embryonic energy reserves, developmental timing, and fecundity in quillback rockfish (Sebastes maliger)

Maternal effects on the quality of progeny can have direct impacts on population productivity. Rockfish are viviparous and the oil globule size of larvae at parturition has been shown to have direct effects on time until starvation and growth rate. We sampled embryos and preparturition larvae opportunistically from 89 gravid quillback rockfish (Sebastes maliger) in Southeast Alaska. Because the developmental stage and sampling period were correlated with oil globule size, they were treated as covariates in an analysis of maternal age, length, and weight effects on oil globule size. Maternal factors were related to developmental timing for almost all sampling periods, indicating that older, longer, and heavier females develop embryos earlier than younger, shorter, or lighter ones. Oil globule diameter and maternal length and weight were statistically linked, but the relationships may not be biologically significant. Weight-specific fecundity did not increase with maternal size or age, suggesting that reproductive output does not increase more quickly as fish age and grow. Age or size truncation of a rockfish population, in which timing of parturition is related to age and size, could result in a shorter parturition season. This shortening of the parturition season could make the population vulnerable to fluctuating environmental conditions.

Length and sex effects on the spatial structure of catches of Pacific halibut (Hippoglossus stenolepis) on longline gear

Field experiments were conducted to test the hypotheses that Pacific halibut (Hippoglossus stenolepis) display small-scale spatial structure within longline catches, relative to other species and empty hooks, or within-species based on sex or length. Sequential hook-by-hook inventories, along with length and sex data, were taken at thirty-one survey stations. Two-dimensional spatial statistics were used to test for 1) aggregation, defined as the clustering of individuals within a given demographic of size or sex over small intervals of distance; and 2) segregation, defined as the sequential occurrence of individuals within a given demographic of size or sex, uninterrupted by other observations, irrespective of the distance between individuals. Statistically significant structure was detected within catches that is more commonly associated with fish length than sex. Significant spatial structuring occurred at 60% of all stations tested. Significant aggregation of halibut of legal length for commercial retention (≥82 cm) was detected at 44% of stations and aggregation of sublegal-size halibut was detected at 11%. Maleand female-based aggregations were observed at 22% and 11% of stations, respectively. Significant segregation of females was observed at 20% of stations, male segregation occurred at 8% of stations, and segregation by size at 16% of stations. Understanding small-scale spatial structure within longline catches may help us interpret changes in survey and commercial catch data. If structure is generated by behavior, then observed size-at-age or relative sex-ratios may be biased relative to underlying distributions. Although physical processes such as gape limitation should remain stable over the time, dynamic processes may be spatially and temporally variabl

Prediction and confirmation of seasonal migration of Pacific sardine (Sardinops sagax) in the California Current Ecosystem

During the last century, the population of Pacific sardine (Sardinops sagax) in the California Current Ecosystem has exhibited large fluctuations in abundance and migration behavior. From approximately 1900 to 1940, the abundance of sardine reached 3.6 million metric tons and the “northern stock” migrated from offshore of California in the spring to the coastal areas near Oregon, Washington, and Vancouver Island in the summer. In the 1940s, the sardine stock collapsed and the few remaining sardine schools concentrated in the coastal region off southern California, year-round, for the next 50 years. The stock gradually recovered in the late 1980s and resumed its seasonal migration between regions off southern California and Canada. Recently, a model was developed which predicts the potential habitat for the northern stock of Pacific sardine and its seasonal dynamics. The habitat predictions were successfully validated using data from sardine surveys using the daily egg production method; scientific trawl surveys off the Columbia River mouth; and commercial sardine landings off Oregon, Washington, and Vancouver Island. Here, the predictions of the potential habitat and seasonal migration of the northern stock of sardine are validated using data from “acoustic–trawl” surveys of the entire west coast of the United States during the spring and summer of 2008. The estimates of sardine biomass and lengths from the two surveys are not significantly different between spring and summer, indicating that they are representative of the entire stock. The results also confirm that the model of potential sardine habitat can be used to optimally apply survey effort and thus minimize random and systematic sampling error in the biomass estimates. Furthermore, the acoustic–trawl survey data are useful to estimate concurrently the distributions and abundances of other pelagic fishes.

Comparative feeding ecology of two elasmobranch species, Squalus blainville and Scyliorhinus canicula, off the coast of Portugal

The small-spotted catshark (Scyliorhinus canicula) (Linnaeus, 1758) and the longnose spurdog (Squalus blainville) (Risso, 1826) are two species occurring in the European and western African continental shelves with a wide geographical distribution. In this study, the diet of S. blainville and S. canicula off the Portuguese western Atlantic coast was investigated in 2006 by collecting monthly samples of these two species from local fishing vessels. In the stomachs of both species, crustaceans and teleosts were the dominant prey items, and molluscs, polychaetes, echinoderms, and sipunculids were found in lower abundance. In S. canicula, urochordate and chondrichthyan species were also observed in stomachs and were classified as accidental prey items. Scyliorhinus canicula consumed a broader group of prey items than did S. blainville. A significant diet overlap was observed, despite both species occupying different depth ranges over the continental shelf. Scyliorhinus canicula exhibited a consistency in diet composition among seasons, sexes, and maturity stages. Nonetheless, for both adults and juveniles, an increase in relative abundance of teleosts in the diet was observed in the spring and summer. This study provides evidence of the importance of S. canicula and S. blainville as benthic and pelagic predators along the western Atlantic coast.

Effect of environmental conditions on the distribution of Pacific mackerel (Scomber japonicus) larvae in the California Current system

We modeled the probability of capturing Pacif ic mackerel (Scomber japonicus) larvae as a function of environmental variables for the Southern California Bight (SCB) most years from 1951 through 2008 and Mexican waters offshore of Baja California from 1951 through 1984. The model exhibited acceptable fit, as indicated by the area under a receiver-operating-characteristic curve of 0.80 but was inconsistent with the zero catches that occurred frequently in the 2000s. Two types of spawners overlapped spatially within the survey area: those that exhibited peak spawning during April in the SCB at about 15.5°C and a smaller group that exhibited peak spawning in August near Punta Eugenia, Mexico, at 20°C or greater. The SCB generally had greater zooplankton than Mexican waters but less appropriate (lower) geostrophic f lows. Mexican waters generally exhibited greater predicted habitat quality than the SCB in cold years. Predicted quality of the habitat in the SCB was greater from the 1980s to 2008 than in the earlier years of the survey primarily because temperatures and geostrophic flows were more appropriate for larvae. However, stock size the previous year had a larger effect on predictions than any environmental variable, indicating that larval Pacific mackerel did not fully occupy the suitable habitat during most years.

Catch rates and demographics of loggerhead sea turtles (Caretta caretta) captured from the Charleston, South Carolina, shipping channel during the period of mandatory use of turtle excluder devices (TEDs)

Trawling was conducted in the Charleston, South Carolina, shipping channel between May and August during 2004–07 to evaluate loggerhead sea turtle (Caretta caretta) catch rates and demographic distributions. Two hundred and twenty individual loggerheads were captured in 432 trawling events during eight sampling periods lasting 2–10 days each. Catch was analyzed by using a generalized linear model. Data were fitted to a negative binomial distribution with the log of standardized sampling effort (i.e., an hour of sampling with a net head rope length standardized to 30.5 m) for each event treated as an offset term. Among 21 variables, factors, and interactions, five terms were significant in the final model, which accounted for 45% of model deviance. Highly significant differences in catch were noted among sampling periods and sampling locations within the channel, with greatest catch furthest seaward consistent with historical observations. Loggerhead sea turtle catch rates in 2004–07 were greater than in 1991–92 when mandatory use of turtle excluder devices was beginning to be phased in. Concurrent with increased catch rates, loggerheads captured in 2004–07 were larger than in 1991–92. Eighty-five percent of loggerheads captured were ≤75.0 cm straight-line carapace length (nuchal notch to tip of carapace) and there was a 3.9:1 female-to-male bias, consistent with limited data for this location two decades earlier. Only juvenile loggerheads ≤75.0 cm possessed haplotypes other than CC-A01 or CC-A02 that dominate in the region. Six rare and one un-described haplotype were predominantly found in June 2004.

Distributions and abundances of Pacific sardine (Sardinops sagax) and other pelagic fishes in the California Current Ecosystem during spring 2006, 2008, and 2010, estimated from acoustic–trawl surveys

The abundances and distributions of coastal pelagic fish species in the California Current Ecosystem from San Diego to southern Vancouver Island, were estimated from combined acoustic and trawl surveys conducted in the spring of 2006, 2008, and 2010. Pacific sardine (Sardinops sagax), jack mackerel (Trachurus symmetricus), and Pacific mackerel (Scomber japonicus) were the dominant coastal pelagic fish species, in that order. Northern anchovy (Engraulis mordax) and Pacific herring (Clupea pallasii) were sampled only sporadically and therefore estimates for these species were unreliable. The estimates of sardine biomass compared well with those of the annual assessments and confirmed a declining trajectory of the “northern stock” since 2006. During the sampling period, the biomass of jack mackerel was stable or increasing, and that of Pacific mackerel was low and variable. The uncertainties in these estimates are mostly the result of spatial patchiness which increased from sardine to mackerels to anchovy and herring. Future surveys of coastal pelagic fish species in the California Current Ecosystem should benefit from adaptive sampling based on modeled habitat; increased echosounder and trawl sampling, particularly for the most patchy and nearshore species; and directed-trawl sampling for improved species identification and estimations of their acoustic target stren

Life-stage recruitment models for Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) on Georges Bank

Ichthyoplankton surveys have been used to provide an independent estimate of adult spawning biomass of commercially exploited species and to further our understanding of the recruitment processes in the early life stages. However, predicting recruitment has been difficult because of the complex interaction of physical and biological processes operating at different spatial and temporal scales that can occur at the different life stages. A model of first-year life-stage recruitment was applied to Georges Bank Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) stocks over the years 1977–2004 by using environmental and densitydependent relationships. The best lifestage mortality relationships for eggs, larvae, pelagic juveniles, and demersal juveniles were first determined by hindcasting recruitment estimates based on egg and larval abundance and mortality rates derived from two intensive sampling periods, 1977–87 and 1995–99. A wind-driven egg mortality relationship was used to estimate losses due to transport off the bank, and a wind-stress larval mortality relationship was derived from feeding and survival studies. A simple metric for the density-dependent effects of Atlantic cod was used for both Atlantic cod and haddock. These life stage proxies were then applied to the virtual population analysis (VPA) derived annual egg abundances to predict age-1 recruitment. Best models were determined from the correlation of predicted and VPA-derived age-1 abundance. The larval stage was the most quantifiable of any stage from surveys, whereas abundance estimates of the demersal juvenile stage were not available because of undersampling. Attempts to forecast recruitment from spawning stock biomass or egg abundance, however, will always be poor because of variable egg survival.

Characterization and expression analysis of TNF-related apoptosis inducing ligand (TRAIL) in grass carp Ctenopharyngodon idella

TRAIL (Apo2 ligand) described as a type II transmembrame protein belonging to the TNF superfamily can induce apoptotic cell death in a variety of cell types. In the present study, a putative cDNA sequence encoding the 299 amino acids of TRAIL (GC-TRAIL) and its genomic organization were identified in grass carp Ctenopharyngodon idella. The predicted GC-TRAIL sequence showed 44 and 41% identities to chicken and human TRAILs, respectively. In a domain search, a tumor necrosis factor homology domain (THD) was identified in the C-terminal portion of TRAILs. The GC-TRAIL gene consists of five exons, with four intervening introns, spaced over approximately 4 kb of genomic sequence. Analysis of GC-TRAlL promoter region revealed the presence of a number of putative transcription factor binding sites, such as Sp1, NF-kappaB, AP-1, GATA, NFAT, HNF, STAT, P53 and IRFI sequences which are important for the expression of other TNF family members. Phylogenetic analysis placed GC-TRAIL and the putative zebrafish (Danio rerio) TRAIL obtained from searching the zebrafish database into one separate cluster near mammalian TRAIL genes, but apart from the reported zebrafish TRAIL-like protein, indicating that the GC-TRAIL is an authentic fish TRAIL. Expression analysis revealed that GC-TRAIL is expressed in many tissues, such as in gills, liver, trunk kidney, head kidney, intestine and spleen. (c) 2005 Elsevier B.V. All rights reserved.

六联苯超薄膜与弱取向外延生长

有机半导体薄膜的形态结构对器件性能具有非常重要的影响，近年来高质量有机半导体薄膜的制备成为有机半导体薄膜器件研究的核心内容之一。弱取向外延生长能够获得类单晶迁移率的高质量有机半导体薄膜。而制备出高取向、大尺寸、低缺陷、连续的高质量外延生长基底是获得类单晶外延薄膜的前提条件，这样就需要深入了解它们的生长行为、生长机理及薄膜相态特性。因此，高质量外延基底生长和弱取向外延生长行为及机理的研究就具有十分重要的理论价值和实用价值，是选择和扩展弱取向外延生长材料体系的基础。由此，本论文中工作主要分为两部分，第一部分工作是对外延基底六联苯超薄膜生长的研究：一方面生长出大尺寸、高取向、连续的超薄膜为弱取向外延生长提供高质量的外延基底，另一方面丰富和发展了有机半导体薄膜生长理论。第二部分工作是对酞菁化合物在六联苯超薄膜上弱取向外延生长行为和机理的研究，为弱取向外延材料体系的选择与扩展提供实验依据和理论指导。 首先，研究了六联苯超薄膜生长行为。研究结果表明：(1) 六联苯超薄膜在高温(＞60 oC)和低温(≤60 oC)的二氧化硅(SiO2)基底上生长具有不同的生长机理：高温时薄膜生长符合扩散受限凝聚生长(DLA)机理，低温时薄膜生长是由低有序薄膜经过亚稳分解后重组向团状岛转变。(2) 六联苯超薄膜的生长行为和相结构表明单层和双层薄膜是两种不同的相态：单层薄膜是高取向的具有液晶特性的薄膜相态，双层薄膜是长程有序的近似体相β-phase结构的结晶相。(3) 通过优化基底温度和生长参数，可以制备出高取向、大尺寸、连续的六联苯超薄膜，即可以为酞菁化合物的弱取向外延生长提供高质量的外延基底。 然后，以平面型自由酞菁(H2Pc)及酞菁锌(ZnPc)和非平面型酞菁氧钒(VOPc)为例，深入研究了酞菁化合物在六联苯超薄膜上的弱取向外延生长行为及机理。研究结果表明：(1) 弱取向外延生长的酞菁分子在六联苯超薄膜上立着生长，p-p共轭的方向平行于基底，同时酞菁分子在薄膜平面内具有规则的取向织构。这种高取向的酞菁化合物薄膜有利于载流子在薄膜平面内的传输，其迁移率达到了相应的单晶水平。(2) 由于六联苯双层及单层薄膜结构和相态的差别，平面型酞菁化合物表现出不同的外延生长行为：在六联苯双层薄膜上生长的酞菁化合物薄膜在薄膜平面内只有一种取向，对应于有公度外延生长(Commensurate Epitaxy)；在六联苯单层薄膜上生长的酞菁化合物薄膜在薄膜平面内有三种取向，同时兼具有公度外延生长和无公度外延生长(Incommensurate Epitaxy)。但非平面型VOPc由于分子排列方式及三斜晶体结构的本质，在六联苯单层及双层薄膜上都只表现出无公度外延生长。(3) 六联苯(001)晶面上突起的氢原子所形成的[110]、[1-10]和[010]沟道对酞菁分子具有强烈的预取向作用，从而形成取向的单分子柱晶核。然后在晶格匹配效应和基底沟道效应下，分别形成有公度外延生长和无公度外延生长。即晶格匹配关系和基底沟道效应为寻找弱取向外延生长有机半导体材料体系提供了理论指导依据。

结构参数对GaN肖特基紫外探测器性能的影响及器件设计

研究了GaN肖特基结构(n~--GaN /n~+-GaN)紫外探测器的结构参数对器件性能的影响机理.模拟计算结果表明:提高肖特基势垒高度和减小表面复合速率,不仅可以增加器件的量子效率,而且可以极大地减小器件的暗电流;适当地增加n~--GaN层厚度和载流子浓度可以提高器件的量子效率,但减小n~--GaN层的载流子浓度却有利于减小器件的暗电流.我们针对实际应用的需要,提出了一个优化器件结构参数的设计方案,特别是如果实际应用中对器件的量子效率和暗电流都有较高的要求,肖特基势垒高度应该≥0.8 eV,n~--GaN层的厚度≥200 nm,载流子浓度1×10~(1)7 cm~(-3) 左右,表面复合速率＜1×10~7 cm/s.

Sequential deprotonation of meso-(p-hydroxyphenyl)porphyrins in DMF: From hyperporphyrins to sodium porphyrin complexes

Sequential deprotonations of meso-(p-hydroxyphenyl)porphyrins (p-OHTPPH2) in DMF + H2O (V/V = 1:1) mixture have been verified to result in the appearance of hyperporphyrin spectra. However, when the deprotonations of these p-OHTPPH2 are carried out in DMF, the spectral changes differ considerably from those in the mixture mentioned above. At low [OH-], the optical spectra in the visible region are still considered to have characteristics of hyperporphyrin spectra. Further deprotonation at much higher basicity makes the optical spectra form three-banded spectra similar to those in the acidic solution. To clarify the molecular origins of these changes, UV-vis, resonance Raman (RR), proton nuclear magnetic resonance (H-1 NMR) experiments are carried out. Our data give evidence that p-OHTPPH2 in DMF can be further deprotonated of pyrrolic-H by higher concentrated NaOH, due to an aprotic medium like DMF effectively weakening the basicity of the porphyrin relative to that of the NaOH, and coordinates with two sodium ions (except the sodium ions that interact with the peripherial phenoxide anions) to form the sodium complexes of p-OHTPPH2 (Na2P, to lay a strong emphasis on the sodium ions that coordinate with the central nitrogen atom), which can be regarded as the porphyrin anions being perturbed by the sodium cations due to their highly ionic character.