bluuebunny/crossref_metadata_2025 huggingface dataset:
Movement Patterns and Stock Composition of Adult Striped Bass Tagged in Massachusetts Coastal Waters
Authors: Kneebone Jeff , Hoffman William S. , Dean Micah J. , Fox Dewayne A. , Armstrong Michael P.
Published: September 2014

The coastal migratory stock of Striped Bass Morone saxatilis has supported fisheries off the Massachusetts (MA) coast for centuries. However, despite this historical importance, limited information is available regarding Striped Bass seasonal movement patterns or migratory pathways within MA coastal waters and beyond. Using passive acoustic telemetry, we evaluated the seasonal residency, coastal migration, and stock composition of 159 adult Striped Bass (65–110 cm TL) by using a network of fixed acoustic receivers deployed from 2008 to 2012 in MA coastal waters and along the U.S. East Coast as part of the Atlantic Cooperative Telemetry (ACT) Network. Seasonal monitoring of tagged individuals indicated that adult Striped Bass were present in MA coastal waters north of Cape Cod annually during May–November, moving into and out of the region via the Cape Cod Canal and along the east side of Cape Cod. Of the 159 tagged individuals, 125 (79%) were detected outside of MA coastal waters by the ACT Network and were observed to make seasonal migrations along the coast to overwintering areas of the mid‐Atlantic and major spawning areas (Chesapeake Bay, Delaware River, and Hudson River). Numerous tagged individuals exhibited interannual fidelity to summer foraging habitat in MA coastal waters, returning to the region for up to 2 years after tagging. Detection of tagged individuals in known spawning areas revealed that Striped Bass from each major stock were present within MA coastal waters during the summer months, with the Chesapeake Bay stock appearing to be the largest contributor to the population from 2008 to 2010. Collectively, these observations suggest that the seasonal population of adult Striped Bass in MA coastal waters has a diversity of origins, demonstrating the importance of the health of each spawning component to the MA seasonal fishery.

Received October 11, 2013; accepted January 23, 2014
Genetic Structure and Diversity of Japanese Chum Salmon Populations Inferred from Single‐Nucleotide Polymorphism Markers
Authors: Sato Shunpei , Templin William D. , Seeb Lisa W. , Seeb James E. , Urawa Shigehiko
Published: September 2014

We estimated the genetic structure and diversity of Japanese Chum Salmon Oncorhynchus keta populations using single‐nucleotide polymorphism (SNP) markers to support the management and assessment of the Japanese salmon hatchery program. A total of 5,571 individuals from 57 Japanese Chum Salmon populations were genotyped with 52 markers. A neighbor‐joining tree, principal coordinate analysis, analysis of molecular variance, and average pairwise FST values indicated the existence of eight regional groups, six in Hokkaido and two in Honshu. Weak but significant isolation by distance was found within the populations of Hokkaido and the Pacific Ocean coast of Honshu. These results suggest that the genetic differentiation among the eight regional groups is small but distinct and occurred through low or restricted gene flow. Furthermore, our results also suggest the persistence of the historical genetic structure (or remnants of it) in extant populations in Japan despite the operation of a hatchery program for about 120 years. The genetic framework of the Japanese Chum Salmon populations that we observed using SNP markers is basically similar to that found by previous studies using other molecular markers but the populations along the western Pacific Ocean coast of Hokkaido are separated into two regional groups.

Received September 19, 2013; accepted February 10, 2014
Fish Assemblages, Connectivity, and Habitat Rehabilitation in a Diked Great Lakes Coastal Wetland Complex
Authors: Kowalski Kurt P. , Wiley Michael J. , Wilcox Douglas A.
Published: September 2014

Fish and plant assemblages in the highly modified Crane Creek coastal wetland complex of Lake Erie were sampled to characterize their spatial and seasonal patterns and to examine the implications of the hydrologic connection of diked wetland units to Lake Erie. Fyke netting captured 52 species and an abundance of fish in the Lake Erie–connected wetlands, but fewer than half of those species and much lower numbers and total masses of fish were captured in diked wetland units. Although all wetland units were immediately adjacent to Lake Erie, there were also pronounced differences in water quality and wetland vegetation between the hydrologically isolated and lake‐connected wetlands. Large seasonal variations in fish assemblage composition and biomass were observed in connected wetland units but not in disconnected units. Reestablishment of hydrologic connectivity in diked wetland units would allow coastal Lake Erie fish to use these vegetated habitats seasonally, although connectivity does appear to pose some risks, such as the expansion of invasive plants and localized reductions in water quality. Periodic isolation and drawdown of the diked units could still be used to mimic intermediate levels of disturbance and manage invasive wetland vegetation.

Received October 1, 2013; accepted March 5, 2014
The Effects of Spatial and Temporal Resolution in Simulating Fish Movement in Individual‐Based Models
Authors: Watkins Katherine Shepard , Rose Kenneth A.
Published: September 2014

Many fisheries management decisions require predictions of spatial dynamics, and simulation of realistic movement is critically important for accurately representing population‐level dynamics with spatially explicit individual‐based models (IBMs). Movement approaches developed to date have been applied across a wide range of spatiotemporal resolutions. We compared four movement approaches or submodels (restricted‐area search, kinesis, event based, and run and tumble) using an IBM (roughly based on Bay AnchovyAnchoa mitchilliand Northern AnchovyEngraulis mordax) that simulated growth, mortality, and movement of a cohort on a two‐dimensional grid. We evaluated the submodels in 2.7‐ × 2.7‐km environments at five resolutions defined by various cell sizes and time steps. We used a genetic algorithm to calibrate each movement submodel over a 300‐generation training phase and then tested the mean movement parameters for a single generation in the training environment and a novel environment. Restricted‐area search, kinesis, and event‐based submodels had higher egg production than a random walk model (baseline, assuming no behavioral movement) across spatiotemporal resolutions in training and novel environments. The run‐and‐tumble submodel also had higher egg production than the random walk model but only under certain conditions. Although restricted‐area, kinesis, and event‐based submodels outperformed random walk at all resolutions, the submodels did not perform equally well across resolutions in terms of egg production and aggregation of model individuals in high‐quality cells (i.e., those with high growth and low mortality). The variability in performance was due to the change in habitat quality experienced by model individuals from one time step to the next. Restricted‐area and event‐based submodels had higher egg production when model individuals experienced small changes in habitat quality, whereas the kinesis and run‐and‐tumble submodels performed better when model individuals experienced larger changes in habitat quality.

Received October 16, 2013; accepted March 11, 2004
Feeding Habits of the Smallscale Fat Snook from East‐Central Florida
Authors: Dutka‐Gianelli Jynessa
Published: September 2014

In general, snook Centropomus spp. are opportunistic carnivores, feeding on fish and crustaceans, as shown by other studies on diets of centropomids in the western Atlantic Ocean. Diet studies for centropomids in Florida refer only to a description of the diet and the ontogenetic shifts in prey preferences of Common Snook C. undecimalis. However, no food habit information for Smallscale Fat Snook C. parallelus is available in Florida. Stomach content analysis and quantitative descriptions of fish diet are important in understanding how species utilize resources, coexist in certain habitats, and possibly share available prey. The objective of this study was to describe the dietary composition for Smallscale Fat Snook in east‐central Florida, in comparison to other diet studies for Smallscale Fat Snook and its congeners. The results show that, like other snook species, Smallscale Fat Snook is a carnivorous species, juveniles feed mainly on penaeid shrimp, and larger fish feed more on varied prey, mainly portunid crabs and teleost species. The diverse diet composition of Smallscale Fat Snook in east‐central Florida suggests that the species is an opportunistic feeder, exploiting locally abundant prey, and feeds in a variety of estuarine and riverine habitats.

Received March 18, 2014; accepted April 17, 2014
Stage‐Structured Simulations Suggest That Removing Young of the Year Is an Effective Method for Controlling Invasive Smallmouth Bass
Authors: Loppnow Grace L. , Venturelli Paul A.
Published: September 2014

Smallmouth Bass Micropterus dolomieu is an invasive fish for which few control methods have been developed or tested. Adult removal is most common, but this strategy is labor‐intensive and can result in an increase in population abundance (i.e., overcompensation). Using a stage‐structured matrix model, we tested removal of young of the year as a control method, both alone and in combination with three supplemental removal strategies. Our results suggest that young of the year removal alone does not lead to overcompensation and can be expected to control some populations of Smallmouth Bass in a reasonable timeframe (e.g., 75% reduction in abundance after 10 years at 68% removal). Lower rates of removal of young of the year are required if this method is combined with supplemental removal strategies (especially those that also target immature bass). Where feasible, we recommend that managers include young of the year removal as part of their control plans. Future research should focus on incorporating more biological realism into simulation models and testing this method in the field.

Received January 15, 2014; accepted April 24, 2014
Evidence of Atlantic Sturgeon Spawning in the York River System
Authors: Hager Christian , Kahn Jason , Watterson Carter , Russo Jay , Hartman Kyle
Published: September 2014

The National Marine Fisheries Service listed five distinct population segments of Atlantic Sturgeon Acipenser oxyrinchus as threatened and endangered under the Endangered Species Act on February 6, 2012. At that time, the only known spawning population of sturgeon in the Chesapeake Bay was in the James River. The goal of this research was to determine whether reproduction was also occurring in the Chesapeake's York River watershed. Based on the assumption that an early fall spawning event occurs in the upper reaches of the watershed, these waters were sampled in late August of 2013 when water temperatures became appropriate for spawning. During a week of sampling, numerous male sturgeon running milt and one spawned‐out female with residual eggs still present were captured. The co‐occurrence of reproductively active males and a recently spawnedout female Atlantic Sturgeon in the upper Pamunkey River at temperatures consistent with documented spawning temperatures in other systems indicates that fall spawning occurs in the York River system. Therefore, the population segment of Atlantic Sturgeon distinct to the Chesapeake Bay has at least two spawning populations that managers should consider when protecting this listed species.

Received November 13, 2013; accepted May 12, 2014
Genetic Composition of the Warm Springs River Chinook Salmon Population Maintained following Eight Generations of Hatchery Production
Authors: Smith Christian T. , French Rod , Lovtang Jens , Hand David
Published: September 2014

Balancing the disparate objectives of fishery augmentation and conservation of an endemic fish population presents a substantial challenge. In the case of Warm Springs National Fish Hatchery (Warm Springs Hatchery), strategies for achieving both objectives included incorporation of natural fish into the hatchery broodstock and restricting proportions of hatchery fish on the spawning grounds. The hatchery has been more successful in implementing the latter than the former. We analyzed 76 single nucleotide polymorphism markers in Spring Chinook Salmon Oncorhynchus tshawytscha collected from the Warm Springs River in 1976–1977 (prior to hatchery production) and 2001–2011 (posthatchery) to examine whether the genetic characteristics of the endemic population had changed during that time. Pre‐ and posthatchery collections clustered together when compared with those from Round Butte Hatchery, which has a nearby segregated program, and other Columbia River populations. The difference between pre‐ and posthatchery collections was nonsignificant, but posthatchery samples exhibited significantly lower expected heterozygosity. We observed some evidence of reduced effective size and increased genetic drift in fish produced at Warm Springs Hatchery (relative to natural‐origin fish) and even stronger evidence of this in fish produced at Round Butte Hatchery. We conclude that natural‐origin Chinook Salmon returning to the Warm Springs River form a distinct group within the interior Columbia Basin spring‐run lineage and have changed very little over the past eight generations. We further speculate that differences between hatchery‐ and natural‐origin fish at Warm Springs Hatchery are expected to increase if hatchery operations remain static (i.e., little integration of natural‐origin fish and incorporation of Round Butte Hatchery fish in the broodstock).

Received February 11, 2014; accepted May 30, 2014
The Effects of Variation in Rearing Conditions on Growth, Smolt Development, and Minijack Rate in Yearling Chinook Salmon: a Hatchery Scale Experiment
Authors: Spangenberg Dina , Larsen Donald A. , Gerstenberger Ryan , Brun Chris , Beckman Brian R.
Published: September 2014

In this investigation a single genetic stock of Hood River, Oregon, Chinook Salmon Oncorhynchus tshawytscha was reared at three different hatchery facilities over three brood years (2008–2010) and monitored for size, growth rate, gill Na+,K+‐ATPase activity, condition factor, whole body energetics, and precocious male maturation (age‐2 minijack rate). This experimental design provided a unique opportunity to isolate environmental from genetic effects on salmonid life history. Differences in the seasonal thermal regimes and associated growth profiles among the three facilities resulted in modest differences in smolt development but significant variation in size at release (range = 18 g body weight, 118 mm FL to 31 g body weight, 142 mm FL) and minijack rates (range = 4.8–57.1%) among groups. Previous studies have found a positive relationship between body size at release and minijack rates. However, in this investigation the release group with the largest mean body size consistently had the lowest minijack rates. This unique result may be due to the more natural thermal regime and feeding profile experienced by fish at this facility compared with that of the other two facilities and highlights the importance and potential benefits of adhering to a more “wildlike” growth profile in hatchery supplementation programs.

Received February 24, 2014; accepted May 29, 2014
A Hierarchical Community Occurrence Model for North Carolina Stream Fish
Authors: Midway Stephen R. , Wagner Tyler , Tracy Bryn H.
Published: September 2014

The southeastern USA is home to one of the richest—and most imperiled and threatened—freshwater fish assemblages in North America. For many of these rare and threatened species, conservation efforts are often limited by a lack of data. Drawing on a unique and extensive data set spanning over 20 years, we modeled occurrence probabilities of 126 stream fish species sampled throughout North Carolina, many of which occur more broadly in the southeastern USA. Specifically, we developed species‐specific occurrence probabilities from hierarchical Bayesian multispecies models that were based on common land use and land cover covariates. We also used index of biotic integrity tolerance classifications as a second level in the model hierarchy; we identify this level as informative for our work, but it is flexible for future model applications. Based on the partial‐pooling property of the models, we were able to generate occurrence probabilities for many imperiled and data‐poor species in addition to highlighting a considerable amount of occurrence heterogeneity that supports species‐specific investigations whenever possible. Our results provide critical species‐level information on many threatened and imperiled species as well as information that may assist with re‐evaluation of existing management strategies, such as the use of surrogate species. Finally, we highlight the use of a relatively simple hierarchical model that can easily be generalized for similar situations in which conventional models fail to provide reliable estimates for data‐poor groups.

Received January 13, 2014; accepted May 5, 2014
Genetic History of Walleyes Spawning in Lake Erie's Cattaraugus Creek: a Comparison of Pre‐ and Poststocking
Authors: Haponski Amanda E. , Dean Hillary , Blake Bevin E. , Stepien Carol A.
Published: September 2014

Fish stocking (artificial supplementation) has been used to augment populations and angling opportunities. However, genetic composition and adaptations of native fish populations may be affected, raising management concerns. From 1995 to 2000, the New York State Department of Environmental Conservation stocked Walleye Sander vitreus fry and fingerlings from the Maumee River (western Lake Erie) into Cattaraugus Creek (eastern Lake Erie). We analyzed nuclear microsatellite (sat) DNA and mitochondrial DNA (mtDNA) variation in Cattaraugus Creek Walleyes for comparisons between prestocking and poststocking groups, among annual spawning runs (1998–2011), among age cohorts, and between sexes. Results for genetic differentiation (index FST) were not significant between prestocking and poststocking groups (sat: FST = 0.003; mtDNA: FST < 0.001), and the two groups did not resemble stocked Maumee River fingerlings (sat: FST = 0.003–0.012; mtDNA: FST = 0.076–0.090). Tests for differentiation were not significant among annual spawning runs (sat: FST = <0.001–0.007; mtDNA: FST = <0.001–0.049), among age cohorts (sat: FST = <0.001–0.006; mtDNA: FST = <0.001–0.097), or between sexes (sat: FST < 0.001; mtDNA: FST < 0.001). Genetic diversity levels were high and consistent (sat: observed heterozygosity [mean ± SE] = 0.71 ± 0.04; mtDNA: haplotype diversity = 0.79 ± 0.01). Thus, despite stocking, the genetic signature of the native spawning run remained distinctive. However, the genetic composition of the local wild population and the stocking source should be assessed prior to any future supplementation plans.

Received December 6, 2013; accepted June 12, 2014
Interoceanic Sex‐Biased Migration in Bluefish
Authors: Miralles L. , Juanes F. , Garcia‐Vazquez E.
Published: September 2014

The BluefishPomatomus saltatrixis a highly migratory species that is composed of different stocks and populations along its nearly cosmopolitan distribution. The Bluefish is the only member of its genus and family, and high migration rates could prevent vicariant speciation across its wide geographical distribution. However, the extent of gene flow between distant populations is unknown. We employed two mitochondrial genes (cytochrome‐coxidase subunit I and cytochromeb) and eight nuclear microsatellite loci to study population structure and infer dispersal of this important commercial and recreational fish across its Northern Hemisphere distribution. Higher gene flow estimates for nuclear loci (of biparental inheritance) than for mitochondrial loci (of maternal inheritance) suggested sex‐biased dispersal, which could be explained by greater female homing or fidelity to spawning sites and greater dispersal of males. Males could contribute more to transoceanic connectivity of Bluefish populations in the North Atlantic Ocean, thus shaping the observed pattern of spatial genetic structure of the Bluefish in its Northern Hemisphere distribution.

Received February 1, 2014; accepted June 9, 2014
Population Origin and Water Temperature Affect Development Timing in Embryonic Sockeye Salmon
Authors: Whitney C. K. , Hinch S. G. , Patterson D. A.
Published: September 2014

Predicting the future impact of changing thermal regimes on life history stages for wild fish requires a better understanding of the relative importance of population origin and offspring size on embryonic development. We assessed hatch timing and offspring size of Sockeye Salmon Oncorhynchus nerka in relation to egg size (variation from full‐sibling families), population origin, and temperature (three treatments of 10, 14, and 16°C). Both hatch timing and hatch duration varied by the interacting effects of population origin and thermal treatment, shown in crossing reaction norms. Hatching was faster, yet more variable, at higher temperatures across many groups, so while fish generally hatched faster, developmental asynchrony also increased among families. On average, fish incubated at 16°C were shorter but not lighter at hatch, showing developmental tradeoffs between basal metabolic requirements and growth. Egg size decreased among populations as migratory distance increased, but development rates were not related to egg size. In this case, embryonic development rates were linked to temperature and population‐specific cues for hatch timing more than to the maternal influence of egg size.

Received March 10, 2014; accepted June 3, 2014
Justification is potential knowledge
Authors: Ichikawa Jonathan Jenkins
Published: September 2014

This paper will articulate and defend a novel theory of epistemic justification; I characterize my view as the thesis that justification is potential knowledge (JPK). My project is an instance of the ‘knowledge-first’ programme, championed especially by Timothy Williamson. So I begin with a brief recapitulation of that programme.
Dietary Supplementation with Allspice Pimenta dioica Reduces the Occurrence of Streptococcal Disease during First Feeding of Mozambique Tilapia Fry
Authors: Yılmaz Sevdan , Ergün Sebahattin
Published: September 2014

Allspice Pimenta dioica as a feed additive was studied for its effects on growth performance and disease resistance in Mozambique Tilapia Oreochromis mossambicus. Five isonitrogenous (36% crude protein) and isocaloric (18.5 kJ/g) diets were formulated to contain 0 (control), 5, 10, 15, or 20 g of allspice/kg of fish feed. In a 50-d feeding trial, 15 plastic tanks (21 L) were stocked with 35 fish fry (0.012 g) each. After the feeding trial, fish were exposed to Streptococcus iniae and mortalities were recorded. The second-order polynomial regression indicated that the dietary allspice level of 10 g/kg provided the best growth performance and feed utilization. The greatest survival after pathogen challenge was also obtained from the diet supplemented with allspice at 10 g/kg. Therefore, allspice acts as a growth promoter to improve feed utilization and weight gain in Mozambique Tilapia fry and acts an antimicrobial agent to enhance disease resistance during first feeding of fry. These results suggest that allspice can be used as an alternative to antibiotics in controlling streptococcal disease in tilapia culture.

Received October 19, 2012; accepted January 20, 2014
Screening Medicinal Plants for Use against Dactylogyrus intermedius (Monogenea) Infection in Goldfish
Authors: Hu Yang , Ji Jie , Ling Fei , Chen Yunhe , Lu Lin , Zhang Qizhong , Wang Gaoxue
Published: September 2014

Methanol extracts of 24 traditional medicinal plants with potential anthelmintic activity against Dactylogyrus intermedius (Monogenea) in Goldfish Carassius auratus were investigated. Abrus cantoniensis, Citrus medica, Dioscorea collettii, and Polygonum multiflorum exhibited 100% activity and were selected for further evaluation by applying five solvents (petroleum ether, chloroform, ethyl acetate, methanol, and water) for the extraction of the samples, followed by an in vivo bioassay. Among the plants tested, water, methanol, and ethyl-acetate extracts of P. multiflorum showed the highest efficacies; EC50 values (median concentration that results in 50% of its maximal effect) were 1.9, 5.4, and 9.1 mg/L, respectively, and extracts showed 100% efficacy against Dactylogyrus intermedius at 100, 12.5, and 25 mg/L. This was followed by ethyl-acetate, chloroform, and methanol extracts of Dioscorea collettii, which demonstrated 100% efficacy at 80, 80, and 120 mg/L and had EC50 values of 19.7, 27.1, and 37.8 mg/L, respectively, after 48 h of exposure. Chloroform and ethyl-acetate extracts of C. medica, which exhibited 100% efficacy against Dactylogyrus intermedius at 100 and 125 mg/L, revealed similar activity and had EC50 values of 58.7 and 51.3 mg/L, respectively. The ethyl-acetate and methanol extracts of A. cantoniensis exhibited the lowest activity and had EC50 values of 279.4 and 64.3 mg/L. Acute toxicities of these active extracts were investigated on Goldfish for 48 h. The findings indicated that extracts of the four plants can be developed as a preferred natural antiparasitic for the control of D. intermedius.

Received June 15, 2013; accepted February 11, 2014
The Effects of a Sublethal Dose of Botulinum Serotype E on the Swimming Performance of Channel Catfish Fingerlings
Authors: Beecham Rachel , Thomas Torri , Gao Dana X. , Gaunt Patricia S.
Published: September 2014

Visceral toxicosis of catfish (VTC) is a disease of cultured Channel Catfish Ictalurus punctatus in the Mississippi Delta region and surrounding states. The etiology of VTC is associated with botulinum serotype E (BoNT/E), which causes blockage of acetylcholine release at the neuromuscular junction, leading to weakness and paralysis of skeletal muscles (including those involved in swimming). This study attempted to determine if sublethal exposure to purified BoNT/E caused reductions in swimming performance and metabolism of Channel Catfish. Catfish swimming performance was assessed on stocker-sized Channel Catfish (mean weight ± SD, 62.35 ± 2.5 g) with 10 sham-injected fish and 10 fish injected with a sublethal dose of BoNT/E. A modified Blazka-type swim chamber was used to assess swimming performance. We injected Channel Catfish with either 0.015% trypsin or 400 pg purified BoNT/E digested with 0.015% trypsin intracoelomically, then acclimated an individual catfish in the swim chamber for 17 h prior to the swimming trial. Water temperature was maintained at ∼28°C, and dissolved oxygen (DO) was between 4 and 7 mg/L. A critical swimming speed (Ucrit) protocol was followed, and DO and temperature were monitored every 2 min throughout the swim trial. Cost of transport was calculated from the oxygen consumption at each test speed (10–70 cm/s). There was a statistical difference between the Ucrits (P = 0.0034), but no differences were found between the cost of transports (P = 0.67) of the sham-injected and BoNT/E groups. There was a difference in the cost of transport as it relates to the speeds tested (P < 0.0001), cost of transports being highest at low speeds and decreasing as speed increased. These results indicate that botulinum E interferes with the swimming speed of the catfish, which could contribute to the mortality from the disease of VTC and potentially make the fish more susceptible to predation.

Received September 20, 2013; accepted February 14, 2014
Microbiological Investigation of Persistent Mortalities in Litopenaeus vannamei Grown in Low Saline Waters in India
Authors: Sanathkumar Hirekudel , Ravi Charan , Padinhatupurayil Suresh Babu , Mol Mini , Prasad Jilagam Krishna , Nayak Binaya Bhusan
Published: September 2014

Microbial diseases are a serious hindrance to successful shrimp aquaculture. The Pacific white shrimp Litopenaeus vannamei is an exotic species recently introduced in India to supplement the failing aquaculture of the Asian tiger shrimp Penaeus monodon due to viral diseases. However, after a brief initial success, the aquaculture of L. vannamei is also experiencing serious problems due to microbial diseases. In this study, we conducted a microbiological investigation into the problem of persistent mortalities in selected L. vannamei farms on the southeastern coast of India. The infected shrimps were positive for the white spot syndrome virus (WSSV) by a nested PCR, though no visible white spots were present on the animals. The shrimps were heavily colonized by Vibrio parahemolyticus, which were isolated from the hepatopancreas, gills, and the body surface. The pond water, despite being low saline groundwater, harbored large numbers of V. parahemolyticus and other Vibrio species, and V. parahemolyticus isolated from L. vannamei were resistant to β-lactam antibiotics and cephalosporins. Our results strongly suggest that the persistent mortalities of L. vannamei were due to a co-infection by V. parahemolyticus and WSSV.

Received December 16, 2013; accepted February 14, 2014
Survival of Fish-Pathogenic Strains of Aeromonas hydrophila under Starvation
Authors: Zhang Xiaojun , Cai Wenlong , Tao Zhen , Arias Cova R.
Published: September 2014

The survival of Aeromonas hydrophila under low-nutrient conditions was investigated in this study. The behavior of three strains isolated from Common Carp Cyprinus carpio (China) and Channel Catfish Ictalurus punctatus (USA) was compared when cells were starved at different temperatures (4, 15, 25, and 35°C) over a 4-week period. Temperature played a major role in cell survival, and cell viability decreased rapidly at 4°C. Conversely, cells stored at 15°C did not lose viability over time. Warmer temperatures (25°C and 35°C) decreased cell numbers by approximately one order of magnitude. Ultrastructural changes in cell morphology were observed in starved cells. Our data confirm that A. hydrophila can persist in the aquatic environment for extended periods, but survival is strongly influenced by temperature.

Received December 13, 2013; accepted March 22, 2014
Cell Culture Medium Inhibits Antigen Binding Used in an ELISA for Detection of Antibodies against Nervous Necrosis Virus
Authors: Choi Bomi , Gye Hyun Jung , Oh Myung-Joo , Nishizawa Toyohiko
Published: September 2014

We investigated the optimum dilution of nervous necrosis virus (NNV) for use as antigens to detect antibodies by an enzyme-linked immunosorbent assay (ELISA) in the Sevenband Grouper Epinephelus septemfasciatus. The ELISA values for a standardized suspension of antigens diluted with L-15 medium containing 1% fetal bovine serum decreased gradually with the dilution of the antigens, whereas those for the antigens diluted with distilled water (DW) initially increased with the dilution of the antigens, peaked at a 320-fold dilution, and then decreased thereafter. Additional studies revealed that binding of NNV antigens to ELISA wells was inhibited by fetal bovine serum and other substances in the L-15 medium. Sera obtained from Sevenband Grouper vaccinated with live NNV vaccine and survivors from natural NNV-infection were subjected to antibody detection by ELISA. All of the sera were positive by ELISA when the standardized suspension was diluted 320-fold, whereas sera from five out of the six survivors and two out of the six vaccinated fish were negative or weakly positive by ELISA using NNV antigens diluted 10-fold. We therefore concluded that cultured NNV solutions prepared in cell culture media may need to be diluted with distilled water for use in ELISA.

Received January 28, 2014; accepted April 16, 2014
Effect of OH depletion on measurements of the mass-to-flux ratio in molecular cloud cores
Authors: Tassis K. , Willacy K. , Yorke Harold W. , Turner Neal J.
Published: September 2014

The ratio of mass and magnetic flux determines the relative importance of magnetic and gravitational forces in the evolution of molecular clouds and their cores. Its measurement is thus central in discriminating between different theories of core formation and evolution. Here, we discuss the effect of chemical depletion on measurements of the mass-to-flux ratio using the same molecule (OH) both for Zeeman measurements of the magnetic field and the determination of the mass of the region. The uncertainties entering through the OH abundance in determining separately the magnetic field and the mass of a region have been recognized in the literature. It has been proposed however that, when comparing two regions of the same cloud, the abundance will in both cases be the same. We show that this assumption is invalid. We demonstrate that when comparing regions with different densities, the effect of OH depletion, in measuring changes of the mass-to-flux ratio between different parts of the same cloud can even reverse the direction of the underlying trends (for example, the mass-to-flux ratio may appear to decrease as we move to higher density regions). The systematic errors enter primarily through the inadequate estimation of the mass of the region.
On the initial propagation of dental caries
Authors: Fabregas Rene , Rubinstein Jacob
Published: September 2014

A multi-dimensional model for dental caries is applied to study the shape of caries lesions in a realistic tooth geometry and to examine the rate of progress of caries. An upgraded model, taking into account the outer prismless enamel layer, is derived and solved. The model demonstrates the importance of this layer in delaying the onset of caries. The conclusions are discussed in light of experimental results.
A local-time-induced unique pointer basis
Authors: Jeknić-Dugić J. , Arsenijević M. , Dugić M.
Published: September 2014

There is a solution to the problem of asymptotic completeness in many-body scattering theory that offers a specific view of the quantum unitary dynamics which allows for the straightforward introduction of local time for every, at least approximately closed, many-particle system. In this approach, time appears as a hidden classical parameter of the unitary dynamics of a many-particle system. We show that a closed many-particle system can exhibit behaviour that is characteristic for open quantum systems and there is no need for the ‘state collapse’ or environmental influence. On the other hand, closed few-particle systems bear high quantum coherence. This local-time scheme encompasses concepts including ‘emergent time’, ‘relational time’ as well as the ‘hybrid system’ models with possibly induced gravitational uncertainty of time.
Experimental study of transport of a dimer on a vertically oscillating plate
Authors: Wang Jiao , Liu Caishan , Ma Daolin
Published: September 2014

It has recently been shown that a dimer, composed of two identical spheres rigidly connected by a rod, under harmonic vertical vibration can exhibit a self-ordered transport behaviour. In this case, the mass centre of the dimer will perform a circular orbit in the horizontal plane, or a straight line if confined between parallel walls. In order to validate the numerical discoveries, we experimentally investigate the temporal evolution of the dimer's motion in both two- and three-dimensional situations. A stereoscopic vision method with a pair of high-speed cameras is adopted to perform omnidirectional measurements. All the cases studied in our experiments are also simulated using an existing numerical model. The combined investigations detail the dimer's dynamics and clearly show that its transport behaviours originate from a series of combinations of different contact states. This series is critical to our understanding of the transport properties in the dimer's motion and related self-ordered phenomena in granular systems.
Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids
Authors: Wirtz Ocana Sabine , Meidl Patrick , Bonfils Danielle , Taborsky Michael
Published: September 2014

Behavioural variation among conspecifics is typically contingent on individual state or environmental conditions. Sex-specific genetic polymorphisms are enigmatic because they lack conditionality, and genes causing adaptive trait variation in one sex may reduce Darwinian fitness in the other. One way to avoid such genetic antagonism is to control sex-specific traits by inheritance via sex chromosomes. Here, controlled laboratory crossings suggest that in snail-brooding cichlid fish a single locus, two-allele polymorphism located on a sex-linked chromosome of heterogametic males generates an extreme reproductive dimorphism. Both natural and sexual selection are responsible for exceptionally large body size of bourgeois males, creating a niche for a miniature male phenotype to evolve. This extreme intrasexual dimorphism results from selection on opposite size thresholds caused by a single ecological factor, empty snail shells used as breeding substrate. Paternity analyses reveal that in the field parasitic dwarf males sire the majority of offspring in direct sperm competition with large nest owners exceeding their size more than 40 times. Apparently, use of empty snail shells as breeding substrate and single locus sex-linked inheritance of growth are the major ecological and genetic mechanisms responsible for the extreme intrasexual diversity observed in
Lamprologus callipterus
.
Temperature acclimation rate of aerobic scope and feeding metabolism in fishes: implications in a thermally extreme future
Authors: Sandblom Erik , Gräns Albin , Axelsson Michael , Seth Henrik
Published: September 2014

Temperature acclimation may offset the increased energy expenditure (standard metabolic rate, SMR) and reduced scope for activity (aerobic scope, AS) predicted to occur with local and global warming in fishes and other ectotherms. Yet, the time course and mechanisms of this process is little understood. Acclimation dynamics of SMR, maximum metabolic rate, AS and the specific dynamic action of feeding (SDA) were determined in shorthorn sculpin (Myoxocephalus scorpius) after transfer from 10°C to 16°C. SMR increased in the first week by 82% reducing AS to 55% of initial values, while peak postprandial metabolism was initially greater. This meant that the estimated AS during peak SDA approached zero, constraining digestion and leaving little room for additional aerobic processes. After eight weeks at 16°C, SMR was restored, while AS and the estimated AS during peak SDA recovered partly. Collectively, this demonstrated a considerable capacity for metabolic thermal compensation, which should be better incorporated into future models on organismal responses to climate change. A mathematical model based on the empirical data suggested that phenotypes with fast acclimation rates may be favoured by natural selection as the accumulated energetic cost of a slow acclimation rate increases in a warmer future with exacerbated thermal variations.
The role of migration in the evolution of phenotypic switching
Authors: Carja Oana , Furrow Robert E. , Feldman Marcus W.
Published: September 2014

Stochastic switching is an example of phenotypic bet hedging, where an individual can switch between different phenotypic states in a fluctuating environment. Although the evolution of stochastic switching has been studied when the environment varies temporally, there has been little theoretical work on the evolution of phenotypic switching under
both
spatially and temporally fluctuating selection pressures. Here, we explore the interaction of temporal and spatial change in determining the evolutionary dynamics of phenotypic switching. We find that spatial variation in selection is important; when selection pressures are similar across space, migration can decrease the rate of switching, but when selection pressures differ spatially, increasing migration between demes can facilitate the evolution of higher rates of switching. These results may help explain the diverse array of non-genetic contributions to phenotypic variability and phenotypic inheritance observed in both wild and experimental populations.
Global malnutrition overlaps with pollinator-dependent micronutrient production
Authors: Chaplin-Kramer Rebecca , Dombeck Emily , Gerber James , Knuth Katherine A. , Mueller Nathaniel D. , Mueller Megan , Ziv Guy , Klein Alexandra-Maria
Published: September 2014

Pollinators contribute around 10% of the economic value of crop production globally, but the contribution of these pollinators to human nutrition is potentially much higher. Crops vary in the degree to which they benefit from pollinators, and many of the most pollinator-dependent crops are also among the richest in micronutrients essential to human health. This study examines regional differences in the pollinator dependence of crop micronutrient content and reveals overlaps between this dependency and the severity of micronutrient deficiency in people around the world. As much as 50% of the production of plant-derived sources of vitamin A requires pollination throughout much of Southeast Asia, whereas other essential micronutrients such as iron and folate have lower dependencies, scattered throughout Africa, Asia and Central America. Micronutrient deficiencies are three times as likely to occur in areas of highest pollination dependence for vitamin A and iron, suggesting that disruptions in pollination could have serious implications for the accessibility of micronutrients for public health. These regions of high nutritional vulnerability are understudied in the pollination literature, and should be priority areas for research related to ecosystem services and human well-being.
Native plant diversity increases herbivory to non-natives
Authors: Pearse Ian S. , Hipp Andrew L.
Published: September 2014

There is often an inverse relationship between the diversity of a plant community and the invasibility of that community by non-native plants. Native herbivores that colonize novel plants may contribute to diversity–invasibility relationships by limiting the relative success of non-native plants. Here, we show that, in large collections of non-native oak trees at sites across the USA, non-native oaks introduced to regions with greater oak species richness accumulated greater leaf damage than in regions with low oak richness. Underlying this trend was the ability of herbivores to exploit non-native plants that were close relatives to their native host. In diverse oak communities, non-native trees were on average more closely related to native trees and received greater leaf damage than those in depauperate oak communities. Because insect herbivores colonize non-native plants that are similar to their native hosts, in communities with greater native plant diversity, non-natives experience greater herbivory.
Control of zinc homeostasis in Agrobacterium tumefaciens via zur and the zinc uptake genes znuABC and zinT
Authors: Bhubhanil Sakkarin , Sittipo Panida , Chaoprasid Paweena , Nookabkaew Sumontha , Sukchawalit Rojana , Mongkolsuk Skorn
Published: September 2014

The Agrobacterium tumefaciens zinc uptake regulator (Zur) was shown to negatively regulate the zinc uptake genes znuABC, encoding a zinc transport system belonging to the ATP-binding cassette (ABC) transporter family, and zinT, which encodes a periplasmic zinc-binding protein. The expression of znuABC and zinT was inducible when cells were grown in medium containing a metal chelator (EDTA), and this induction was shown to be specific for zinc depletion. The expression of znuABC was reduced in response to increased zinc in a dose-dependent manner, and zinT had a less pronounced but similar pattern of zinc-regulated expression. The inactivation of zur led to constitutively high expression of znuABC and zinT. In addition, a zur mutant had an increased total zinc content compared to the WT NTL4 strain, whereas the inactivation of zinT caused a reduction in the total zinc content. The zinT gene is shown to play a dominant role and to be more important than znuA and znuB for A. tumefaciens survival under zinc deprivation. ZinT can function even when ZnuABC is inactivated. However, mutations in zur, znuA, znuB or zinT did not affect the virulence of A. tumefaciens.
Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage
Authors: Hagmann Joerg , Becker Claude , Müller Jonas , Stegle Oliver , Meyer Rhonda C , Schneeberger Korbinian , Fitz Joffrey , Altmann Thomas , Bergelson Joy , Borgwardt Karsten , Weigel Detlef
Published: September 2014

There has been much excitement about the possibility that exposure to specific environments can induce an ecological memory in the form of whole-sale, genome-wide epigenetic changes that are maintained over many generations. In the model plant Arabidopsis thaliana, numerous heritable DNA methylation differences have been identified in greenhouse-grown isogenic lines, but it remains unknown how natural, highly variable environments affect the rate and spectrum of such changes. Here we present detailed methylome analyses in a geographically dispersed A. thaliana population that constitutes a collection of near-isogenic lines, diverged for at least a century from a common ancestor. We observed little DNA methylation divergence whole-genome wide. Nonetheless, methylome variation largely reflected genetic distance, and was in many aspects similar to that of lines raised in uniform conditions. Thus, even when plants are grown in varying and diverse natural sites, genome-wide epigenetic variation accumulates in a clock-like manner, and epigenetic divergence thus parallels the pattern of genome-wide DNA sequence divergence.
Genome-wide map of regulatory interactions in the human genome
Authors: Heidari Nastaran , Phanstiel Douglas H. , He Chao , Grubert Fabian , Jahanbani Fereshteh , Kasowski Maya , Zhang Michael Q. , Snyder Michael P.
Published: September 2014

Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. Bound regions covered 80% of DNase I hypersensitive sites including 99.7% of TSS and 98% of enhancers. Correlating this map with ChIP-seq and RNA-seq data sets revealed cohesin, CTCF, and ZNF143 as key components of three-dimensional chromatin structure and revealed how the distal chromatin state affects gene transcription. Comparison of interactions between cell types revealed that enhancer–promoter interactions were highly cell-type-specific. Construction and comparison of distal and proximal regulatory networks revealed stark differences in structure and biological function. Proximal binding events are enriched at genes with housekeeping functions, while distal binding events interact with genes involved in dynamic biological processes including response to stimulus. This study reveals new mechanistic and functional insights into regulatory region organization in the nucleus.