Application of sperm cryopreservation in selective breeding of the Pacific oyster,Crassostrea gigas (Thunberg)

The robustness of Pacific oyster, Crassostrea gigas (Thunberg), sperm cryopreservation in the context of selective breeding based on family lines was investigated. Irrespective of egg density, high fertilization success was achieved with cryopreserved sperm when sperm:egg ratios of 1000:1 to 10 000:1 were used. Variation among replicate runs on the same oyster batches was minimal, indicating that cryopreservation and larval rearing procedures were repeatable. Twenty independent single male–female crosses were made to assess the utility of cryopreserved sperm in selective breeding. The fertility of unfrozen sperm was generally a poor predictor of cryopreserved sperm fertility. Based on D‐larval yields, 17 of the 20 crosses were likely to yield adequate spat for selective breeding (>10⁵ D‐larvae from 1 million eggs), two were marginal (5 × 10⁴ D‐larvae) and one was inadequate (4 × 10³ D‐larvae). An alternative fertilization strategy to improve D‐yield from a given number of sperm was then tested. Fertilizing 10 million eggs at a sperm:egg ratio of 200:1 increased the total D‐yield when compared with fertilizing 1 million eggs at a sperm:egg ratio of 2000:1 for the same male–female pair. We conclude that, despite wide variation in fertility, cryopreserved sperm is useful for family production.     

The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes

Background  

High quality annotation of the genes and transposable elements in complex genomes requires a human-curated integration of multiple sources of computational evidence. These evidences include results from a diversity of ab initio prediction programs as well as homology-based searches. Most of these programs operate on a single contiguous sequence at a time, and the results are generated in a diverse array of readable formats that must be translated to a standardized file format. These translated results must then be concatenated into a single source, and then presented in an integrated form for human curation.     

Comparing theoretical irrigation requirement and actual irrigation for citrus in Florida

Florida ranks first in citrus production, with nearly 68% of all U.S. citrus growing in the season 2005-2006. Most of the citrus groves are located from central to south Florida, and agricultural irrigation permitting is regulated by three of Florida's five water management districts. Most of the permitting for citrus production in Highlands, Polk and Hillsborough counties is conducted by the Southwest Florida Water Management District (SWFWMD), and quantities are based on the District's AGMOD computer program. In 2003, the SWFWMD implemented new permit criteria so that permitted amounts were more representative of actual water use. This paper compares grower reported citrus irrigation water use in Highlands, Polk and Hillsborough counties from 1994 through 2005 with permitted and theoretical irrigation requirements calculated by a daily water balance. Two different sets of crop coefficients (K_c's) developed for citrus in Florida were compared in the daily soil water balance calculation of theoretical irrigation requirements. The percentage of irrigated area considered in this study ranged from 40 to 60% to simulate a range of grower practices. Meteorological data from two weather stations and additional rainfall information from 50 locations within the three counties was used in the water balance. Missing and error values in the meteorological historical record data were filled with weather generators. The multiannual average water consumption (including cold protection water use) from growers ranged from 243 (Hillsborough) to 406 mm (Highlands) and the multiannual average permitted irrigation requirement (without cold protection) ranged from 295 to 557 mm. The simulated gross irrigation requirements under different scenarios of location-K_c-wetted area were variable but mostly lower than the limits established by the district, except for some scenarios in Polk County, whose maximum simulated irrigation value reached 578 mm year⁻¹. In general, permitted limits recommended by the SWFWMD seem to be reasonable for the actual water use by growers in these counties.     

Changes in epidemiological patterns of sea lice infestation on farmed Atlantic salmon, Salmo salar L., in Scotland between 1996 and 2006

Analyses of a unique database containing sea lice records over an 11 year period provide evidence of changing infestation patterns in Scotland. The data, collected from more than 50 commercial Atlantic salmon farms, indicate that both species of sea lice commonly found in Scotland, Lepeophtheirus salmonis and Caligus elongatus, have declined on farms over the past decade. Reductions for both species have been particularly marked since 2001 when more effective veterinary medicines became available. Treatment data were also available in the database and these show a growing trend towards the use of the in-feed medication emamectin benzoate (Slice), particularly in the first year of the salmon production cycle. However, this trend towards single product use has not been sustained in 2006, the latest year for which data are available. There is some evidence of region to region variation within Scotland with the Western Isles experiencing higher levels of infestation. However, compared to the levels observed between 1996 and 2000, all regions have benefited from reduced lice infestation, with the overall pattern showing a particular reduction in the second and third quarters of the second year of production.     

Loggerhead turtle (Caretta caretta) bycatch in Canadian pelagic longline fisheries: Relative importance in the western North Atlantic and opportunities for mitigation

Little is known about the ecology of loggerhead turtles, Caretta caretta, in Canadian waters. However, Canada's eastern waters off the Scotian Shelf, Georges Bank and Grand Banks appear to be seasonal foraging habitats based on dates and locations where they have been captured as fishery bycatch. Estimates derived from data recorded by the international observer program (IOP) and used for this study suggest that thousands of mostly immature loggerheads have been captured in the Canadian pelagic longline fishery (PLF) in the western North Atlantic since 1999. These data suggest that the PLFs for tuna and swordfish are among the most important causes of incidental capture. Although U.S. and Canadian bycatch estimation methods differ and uncertainty associated with the estimates is high, it is clear from the IOP data that bycatch in the Canadian PLF is substantial and roughly within the same magnitude as that reported for the entire U.S. fleet in the North Atlantic for the same period (1999–2005). Analysis of bycatch observer data from the Canadian PLF and other empirical data suggests that fishing at temperatures below 20 °C using fish rather than squid bait and size-18 circle hooks could reduce loggerhead bycatch and mortality. However, research is needed to identify the best options and their commercial viability. Loggerheads that use Canadian Maritime waters are one of the least studied groups of loggerheads in the world, so systematic long-term studies on the ecology of loggerheads in Canada would help fill important information gaps and assist in developing effective recovery plans for this species.     

Minimizing Fish Oil and Fish Meal with Plant‐based Alternatives in Sunshine Bass Diets without Negatively Impacting Growth and Muscle Fatty Acid Profile

We determined whether canola oil could spare menhaden oil (MO) in diets containing minimal fish meal without affecting sunshine bass, Morone chrysops × Morone saxatilis, production. Seven isonitrogenous, isocaloric (41.7% crude protein and 14.6% crude lipid) diets containing graded levels (0, 20, 40, 60, 80, or 100%) of menhaden to canola oils with 20% menhaden meal (MM) or 100% canola oil with 20% lipid‐extracted MM were fed to sunshine bass (initial weight 9.3 ± 0.16 g; mean ± SD) twice daily to apparent satiation for 10 wk. Sunshine bass fed less than 40% of their dietary lipid as MO exhibited significantly (P < 0.05) lower feed intake and growth rates. Increased concentrations of saturated, n‐3, and n‐3 highly unsaturated fatty acids (FA) in the fillet were associated with MO‐rich diets, while monounsaturated and n‐6 FA were most common in fillets from fish fed diets rich in canola oil. Reducing MO to 40% of the dietary lipid in diets containing minimal fish meal allows for efficient utilization of marine resources without negatively impacting juvenile sunshine bass production.     

Effects of transition season management on soil N dynamics and system N balances in rice–wheat rotations of Nepal

In the low-input rice–wheat production systems of Nepal, the N nutrition of both crops is largely based on the supply from soil pools. Declining yield trends call for management interventions aiming at the avoidance of native soil N losses. A field study was conducted at two sites in the lowland and the upper mid-hills of Nepal with contrasting temperature regimes and durations of the dry-to-wet season transition period between the harvest of wheat and the transplanting of lowland rice. Technical options included the return of the straw of the preceding wheat crop, the cultivation of short-cycled crops during the transition season, and combinations of both. Dynamics of soil N_min, nitrate leaching, nitrous oxide emissions, and crop N uptake were studied throughout the year between 2004 and 2005 and partial N balances of the cropping systems were established. In the traditional system (bare fallow between wheat and rice) a large accumulation of soil nitrate N and its subsequent disappearance upon soil saturation occurred during the transition season. This nitrate loss was associated with nitrate leaching (6.3 and 12.8 kg ha⁻¹ at the low and high altitude sites, respectively) and peaks of nitrous oxide emissions (120 and 480 mg m⁻² h⁻¹ at the low and high altitude sites, respectively). Incorporation of wheat straw at 3 Mg ha⁻¹ and/or cultivation of a nitrate catch crop during the transition season significantly reduced the build up of soil nitrate and subsequent N losses at the low altitude site. At the high altitude site, cumulative grain yields increased from 2.35 Mg ha⁻¹ with bare fallow during the transition season to 3.44 Mg ha⁻¹ when wheat straw was incorporated. At the low altitude site, the cumulative yield significantly increased from 2.85 Mg ha⁻¹ (bare fallow) to between 3.63 and 6.63 Mg ha⁻¹, depending on the transition season option applied. Irrespective of the site and the land use option applied during the transition season, systems N balances remained largely negative, ranging from −37 to −84 kg N ha⁻¹. We conclude that despite reduced N losses and increased grain yields the proposed options need to be complemented with additional N inputs to sustain long-term productivity.     

An investigation into the bacterial aetiology of 'black patch necrosis' in Dover sole, Solea solea L.

Abstract. A recurring disease known as 'black patch necrosis' (BPN) has been the cause of severe mortalities in 0-group and 1-group Dover sole during the period 1974-1978 at the Sea Fish Industry Authority's Marine Cultivation Unit at Hunter-ston, Ayrshire, Scotland. Samples of diseased and healthy Dover sole tissue were examined microbiologically and a long thin filamentous Gram-negative organism, strongly resembling Flexibacter columnar's , was repeatedly isolated from diseased tissue but was not found in healthy tissue. This organism was pathogenic to Dover sole, producing 100% mortality in 96 h at 17.5°C (±2°C) and the organism was reisolated from all the infected fish. The pathogenic isolate and reisolate were examined and compared with reference strain NCMB 1038 of Flexibacter columnarts , formerly known as Chondrococcus columnaris or Cytophaga columnaris. The isolate, reisolate and type culture were identical with respect to cell morphology, oxidase test, catalase production, production of H₂S, casein hydrolysis, gelatin liquefaction, hydrolysis of Tween 20, degradation of tyrosine and starch hydrolysis. All bacterial types showed similar patterns of sensitivity to a range of antibiotics. It is proposed that a Flexibacter columnari's-like organism is associated with the condition in farmed Dover sole known as 'black patch necrosis'.     

Method for Determining Apparent Digestibility of Carbohydrate and Protein Sources for Artificial Diets for Juvenile Sea Cucumber,Australostichopus mollis

Effective nursery diets can greatly reduce the cost of producing juvenile sea cucumbers for release to aquaculture or restocking programs. However, methods for systematically testing the bioavailability of artificial diet ingredients for sea cucumbers are poorly developed, and consequently, there has been little research in this field. The current study presents methods developed to test the suitability of common carbohydrate and protein sources for inclusion in artificial diets for juvenile Australostichopus mollis. Apparent digestibility of carbohydrates was moderate and did not exceed 50% for any carbohydrates assayed. Wheat starch and carrageenans showed the highest digestibility amongst carbohydrates. Differences in apparent digestibility were not reflected in growth performance of juvenile A. mollis fed carbohydrate diets; overall growth performance was poor for all diets. Artificial protein sources consistently exhibited higher apparent digestibility, ranging from 75.1% for fish meal to 98.1% for casein. Low‐cost protein sources, like meat meal, show promise for future use in artificial diet formulation. However, delivering high protein content may reduce ingestion rates and thereby lower overall digestive efficiency in juveniles. Results show that artificial carbohydrate sources have some potential as diet constituents for juvenile sea cucumbers but are unsuitable as primary energy sources. Future testing of artificial carbohydrate sources for A. mollis may require predigestion to improve digestibility.     

Evaluation of Streptocephalus dichotomus nauplii as a larval diet for freshwater prawn Macrobrachium rosenbergii

This study was performed to assess the nutritional value of Streptocephalus dichotomus nauplii and compared with standard larval diet and parthenogenetic strain of Artemia nauplii. The effectiveness of live feed was determined by feeding freshwater prawn Macrobrachium rosenbergii postlarvae. Results on the growth rate, weight gain, survival, fatty acid and amino acid composition show a significant variation between the dietary treatments. Mean larval growth was significantly different ( P  < 0.001) between control diet (13.5 ± 0.5 mm) and live feeds ( Streptocephalus nauplii; 18.4 ± 0.5 mm and Artemia nauplii 18.7 ± 0.2 mm). The weight of larvae-fed Streptocephalus (41.1 ± 1.44 mg) and Artemia nauplii (41.7 ± 0.2 mg) was not significantly different; however, treatment with live feeds was significantly higher than the control (16.3 ± 0.5 mg) ( P  < 0.001). Proximate composition on the fairy shrimp reveals that they are rich in protein, lipid, essential amino acids (EAA) and essential fatty acids (EFA). The polyenoic unsaturated fatty acid (18 : 2 n-6 and 18 : 3 n-3) and highly unsaturated fatty acid (20 : 4 n-3 and 20 : 5 n-3) show a dramatic increase in larval tissue relative to its proportional composition in the live diets. Amino acid composition in the live feeds, Streptocephalus and Artemia nauplii, perfectly reflects on the amino acid proportions in the larvae-fed diets which confirm its utilization.