Production of positive controls for calcivirus-specific PCR using recombinant baculiovirus technology

Recent advances in our knowledge of the genetic structure of human caliciviruses (HuCVs) and small round-structured viruses (SRSVs) have led to the development of polymerase chain reaction (PCR)-based molecular tests specific for these viruses. These methods have been developed to detect a number of human pathogenic viruses in environmental samples including water, sewage and shellfish. HuCVs and SRSVs are not culturable, and no animal model is currently available. Therefore there is no convenient method of preparing viruses for study or for reagent production. One problem facing those attempting to use PCR-based methods for the detection of HuCVs and SRSVs is the lack of a suitable positive control substrate. This is particularly important when screening complex samples in which the levels of inhibitors present may significantly interfere with amplificiation. Regions within the RNA polymerase regions of two genetically distinct human caliciviruses have been amplified and used to produce recombinant baculoviruses which express RNA corresponding to the calicivirus polymerase. This RNA is being investigated as a positive control substrate for PCR testing, using current diagnostic primer sets. Recombinant baculovirus technology will enable efficient and cost-effective production of large quantities of positive control RNA with a specific known genotype. We consider the development of these systems as essential for successful screening and monitoring applications.

The production of freshwater fish for food

It has been estimated that in England and Wales fresh water covers some 340 square miles of which about one quarter is inhabited mainly by salmon and trout; in Scotland the lakes cover an area of 340 square miles. The principal object of this publication is to make available in handy form some of the methods, especially those involving the use of manures, by which crops of fish from water can be increased. The cultivation of water which this implies may be compared directly to the cultivation of farm land: the conditions for growth are made as favourable as possible, the seed is sown in the form of young fish, and after one or perhaps two growing seasons the crop is harvested. There are however many waters about the country where marketable fish are already available and can be removed without prejudice to, and indeed to the advantage of, sporting fisheries. In such cases it is necessary only to remove the fish and to rely on the natural processes of reproduction of those which are left to repopulate the water. Farming waters in the true sense is the concern of the greater part of this publication; the removal of crops of otherwise unwanted fish is considered in the last two sections on perch trapping and eel fisheries.

Diel and seasonal timing of sound production by black drum (Pogonias cromis)

Acoustic recorders were used to document black drum (Pogonias cromis) sound production during their spawning season in southwest Florida. Diel patterns of sound production were similar to those of other sciaenid fishes and demonstrated increased sound levels from the late afternoon to early evening—a period that lasted up to 12 hours during peak season. Peak sound production occurred from January through March when water temperatures were between 18° and 22°C. Seasonal trends in sound production matched patterns of black drum reproductive readiness and spawning reported previously for populations in the Gulf of Mexico. Total acoustic energy of nightly chorus events was estimated by integration of the sound pressure amplitude with duration above a threshold based on daytime background levels. Maximum chorus sound level was highly correlated with total acoustic energy and was used to quantitatively represent nightly black drum sound production. This study gives evidence that long-term passive acoustic recordings can provide information on the timing and location of black drum reproductive behavior that is similar to that provided by traditional, more costly methods. The methods and results have broad application for the study of many other fish species, including commercially and recreationally valuable reef fishes that produce sound in association with reproductive behav

Assessing trends in the density of Atlantic croaker (Micropogonias undulatus): a comparison of passive acoustic and trawl methods

Using data collected simultaneously from a trawl and a hydrophone, we found that temporal and spatial trends in densities of juvenile Atlantic croaker (Micropogonias undulatus) in the Neuse River estuary in North Carolina can be identified by monitoring their sound production. Multivariate analysis of covariance (MA NCOVA) revealed that catch per unit of effort (CPUE) of Atlantic croaker had a significant relationship with the dependent variables of sound level and peak frequency of Atlantic croaker calls. Tests of between-subject correspondence failed to detect relationships between CPUE and either of the call parameters, but statistical power was low. Williamson’s index of spatial overlap indicated that call detection rate (expressed by a 0–3 calling index) was correlated in time and space with Atlantic croaker CPUE. The correspondence between acoustic parameters and trawl catch rates varied by month and by habitat. In general, the calling index had a higher degree of overlap with this species’ density than did the received sound level of their calls. Classification and regression tree analysis identified calling index as the strongest correlate of CPUE. Passive acoustics has the potential to be an inexpensive means of identifying spatial and temporal trends in abundance for soniferous fish species.

Fishing gear and methods of the river Brahmaputra in Assam

Potentially the inland fishery resources of the country are of very high order. But the present level of their exploitation is far from optimum, mainly because of the inadequacies of the existing fishing gear and methods. There is vast scope for increasing the fish production from inland waters by improving the existing gear and methods. This would require a thorough study of the fishing gear and methods in vogue, of which very little is known at present. In the present communication the authors discuss the fishing gear and methods of the river Brahmaputra, in Assam, based on a survey carried out by them during January-February 1964. The survey covers a 640 km stretch of the Brahmaputra River, its important tributaries and connected bheels, from Dhubri to Dibrugarh. As a result of the survey about 19 types of fishing nets, which could be grouped into eight classes, were identified. The salient technological features of the gears and their methods of operation are discussed class-wise. The characteristics of the individual types are shown in tables. The materials used for gear and gear accessories, are briefly discussed. The classification and relative importance of different types of gear are examined. Besides, the influence of the ecological and topographical features of the river on the development of different types of fishing gears, is also discussed.

Study of the relative effectiveness of extension methods in educating fisherwomen

Three experimental groups from three different fishing villages were selected and administered with three extension treatments on two messages, namely, production of fish wafers and fish pickles. There was a significant knowledge gain in the subjects taught through different extension methods. It was observed that lecture aided with slides induced maximum knowledge followed by lecture aided with charts and lecture alone. Among all, the young and highly educated women gained maximum knowledge.

Diversity, abundance distribution and secondary production of intertidal and subtidal benthic macrofauna of Bushehr Province with emphasis on annelida groups

The present investigation was undertaken to establish a reference situation for future use, to identify temporal and spatial composition of macrofauna and estimate some ecological indices in the sub tidal waters along the Bushehr coastal waters in Persian Gulf. Six transects were selected including Genaveh, Farakeh, Shif, Bandargah, Rostami and Asalouyeh, at each transect 3 station were sampled in depths of zero, 5 and 10 metres. Sampling was seasonally carried out by a VAN VEEN grab 0.0225 m2, during summer 2008 until spring 2009. Samples were wet sieved immediately using 0.5 mm mesh size sieves and sediment retained in the sieve was preserved in 4% buffered formalin solution. Macrofauna specimen were separated from the sediments using decantation and elutriation methods, enumerated and identified up to the Genus level. Environmental factors such as temperature. pH, and salinity were recorded in field using sensitive probs and refractometer (for salinity) and also sediment samples were taken for TOM and grain size analysis in all the stations. 5611 specimens belonging to 66 genera were collected during the present study. Polychaetes were dominant both in terms of genus number (31) and relative abundance (74 % of total macrofaunal abundance). The other dominant groups were Artheropoda, (16.1%), Molusca (2.8%), Echinodermata (1.29%) and others including Nematoda, Nemertina, Echiura and Turbellaria (5.8%). Thirty one Genera belong of 27 families of polychaeta, one genus and family of Subphylum Chlicerata,19 genera belong to 14 families of Crustacea, 8 genera belong to 6 families of Molusca, were indentified in the studied region. 1 family (Polygordidae) and 3 genera (Flabeligera, Pilargis and Polygordius) of Polychaeta, 1 family (Nymphonidae) and genus (Nymphon) of Chelicerata, 1 Family (Nematoplanidae) and genus (Nematoplana) of Turbellaria, were identified for the first time in Persian Gulf area. The result indicated that macrofauna organism have strong relationship with the grain size characteristics of the sediments they inhabit. The most surface deposit feeder specimens such as Prionospio and Cossura were found in zero meters depth of Genaveh, Farakeh, Bandargah, Rostami and Asalouyeh stations with sandy substratum, however the most burrowing deposit feeder and scavenger specimens such as Capitella and Petaloproctus were collected in 5 and 10 meter depths of stations with silty–clay substratum. The annual mean abundance, Shanon- weiner diversity and evenness of macrofauna were estimated1152.73 N/ m² , 2.72 and 0.792 respectively .The annual average biomass and secondary production were computed 1.797 gDW m² and 3.594 gDW m² y-1 .The average of water temperature, salinity, pH and oxygen concentration were recorded between 16.37-36.05 °C, 38-42 g/l, 7.89-8.76 and 4.23-8.23 mg/l, respectively during this study in 6 studied region. Among of investigated stations Asalouyeh adjacent of effluent canal of Gas and petrochemical industry sewage and Farakeh regions adjacent the Helleh estuary had the lowets and the highest community indices. The average of diversity and density in 5 meters depth stations with moderate of sand, silt and clay were slightly more than 2 other depths stations, it seems that 5 meters stations are made a transition habitats between 2 sandy and clay habitats, that can be used by 2 groups of surface and borrowing deposit feeders. Based on the data provided in this survey, the temperature variation, sediment texture, TOM, type habitat and manmade factors of Gas and petrochemical industries have had the most effect on the macrofauna community structure in the studied region during sampling periods.

Suitability of commercially available Bacillus probiotics on growth, survival and production of black tiger shrimp (Penaeus monodon Fab.)

Different forms of Bacillus probiotics was assessed in the earthen ponds on tiger shrimp (Penaeus monodon) culture. The experiment was designed with three different treatments depending on the mode of application (T1=oral probiotics; T2=spreading probiotics and T3=oral+ spreading probiotics). The shrimp was cultured for 120 days with the stocking density of 6-PL/m².Oral probiotics in the respective ponds were supplied with feeds. Whereas, spreading probiotics was applied to the pond water during pond preparation at 30, 60 and 90 days of culture period. Results of the experiment revealed that, all forms of Bacillus probiotic had effective role to keep the culture environment friendly in terms of mineralization of organic matter, nitrogen and phosphorus content in bottom sediment; holding of water transparency in a congenial state, increasing the density of planktonic biomass and boosting the THB-Vibrio ratio in water and sediment with insignificance (p>0.05) difference between different treatments. Whilst, spreading form of Bacillus pro biotic showed higher weight gain (27.58±1.18g), survival rate (70.75±8.54%) and production (1167.66±109.62 kg/ha) and expected lower FCR (1.81 ±0.06) values with significant difference (p<0.01) with others methods of application, indicated its superiority in tiger shrimp culture.

An assessment of handling and processing methods used for the shrimp fishery by-catch in Kalpitiya, Sri Lanka

The by-catch from the shrimp trawl fishery in Kalpitiya is mainly used for the production of dried fish, which provides an additional source of income for fishermen in the area. It has been observed that current handling practices along the value addition chain are responsible for the poor quality and low price of the end product. This study was aimed at identifying the shortcomings in such handling practices by fishermen and dried fish producers and assessing the quality of shrimp fishery by-catch along the processing chain in order to recommend more efficient utilization methods that will improve the quality of the end product. Fresh fish, dried fish and harbour water samples were tested for total coli forms, faecal coliforms, E. coli and Salmonella in order to assess their microbial quality: In addition, standard plate counts (SPC) of fish samples were also carried out. A survey was carried out from July-October 2006 at Kalpitiya, using a pre-tested questionnaire to collect information from individuals who have been engaged in dried fish processing. Average values obtained for freshly landed and dried fish respectively, were, SPC 9.88x10 super(5) CFU/g and 30.43x10 super(5) CFU/g, total coliforms 23.05 and 24.23 MPN/g and fecal coliforms 8.28 and 9.00 MPN/g. These values exceed the recommendations in the SL standards. A quarter of the landed fresh fish and 38% of dried fish from the producers were positive for E. coli and thus failed to show required end product quality. SPC of harbour water was 14.35x10 super(6) CFU/ml and all samples were found to be contaminated with E. coli. None of the fishermen and dried fish producers were satisfied with the quality of the end product. The reasons for poor quality as indicated by them were: limited availability of ice (75%), lack of infrastructure facilities (65%), uncertainty of markets (52%), lack of emphasis on quality (47%) and poor access to available technologies (41%). Respondents to the questionnaire also identified: unavailability of potable water, insulated boxes, good landing jetty, racks for drying fish, poor cold storage facilities and limitations in dried fish storage facilities, as further factors leading to the loss of quality in their products. Results demonstrate that improvements to the infrastructure facilities and conducting of proper awareness programmes on handling practices could lead for improvements in the quality of value added products prepared from the shrimp fishery by-catch at Kalpitiya.

Possible fish stock size assessment and available production survey as developed on Lake Kariba

This paper is an outline of methods practically useful for the evaluation of ichthyomass, fish abundance, available production and yield in lakes and rivers. Terms and concepts are reviewed, and difficulties stemming from the use of "predetermined" mathematical models are discussed. Sampling with toxicants in blocked-off areas was found to be the most practical method and is described in detail. For the total estimation of ichthyomass the spatial ranges of fish distribution must be determined; the results of echo-sounding surveys for horizontal, vertical, topographical, seasonal and diel fish distribution are given. Some of the most important methods for computing available production are listed and applied to Lake Kariba as an example. In particular, a method based on the balance between the main predator and prey species is reviewed. The ecological production survey concept is finally stressed as applied to multispecies fish stocks.

Fishery methods and fish diversity in the Kilombero River in south-eastern Tanzania

Assessment of common fishery methods and of fish diversity was undertaken in two fishing camps on the Kilombero River in south-eastern Tanzania in surveys towards the end of the dry season, 1994. Fishermen identified 23 different types of fish that they caught on a regular basis. Only 19 species of fish, belonging to 17 genera and 11 families were, however, identified according to Linnean taxonomy. Hooks, nets, traps and spears were used to catch fish. Fish were either sold fresh. or preserved for storage and long-distance tranport by smoking or frying. based un frequency distributions of the numbers of fish landed over a 4 day period at one of the camps, a Shannon-diversity index of 1.95 was calculted. The fork (or total) length of 480 fish and the weight of 413 fish were measured and length frequency distributions as well as length-weight relationships determined for the six most common species. It is concluded that local fishing methods applied in the Kilombero River allow for sustainable fish production.