Development of an assay to determine single nucleotide polymorphisms in the prion gene for the genetic diagnosis of relative susceptibility to classical scrapie in sheep.

The objective of this study was to develop a reliable Taqman 5' Nuclease Assay for genotyping sheep for scrapie susceptibility. The sheep prion gene contains 2 single nucleotide polymorphisms (SNPs) that may mediate resistance to classical scrapie, one at codon 136, alanine (A) or valine (V), and another at codon 171, arginine (R) or glutamine (Q). The R allele appears to confer resistance to classical scrapie, with the AA(136) RR(171) genotype the most resistant to scrapie and QR(171) only rarely infected in the US sheep population. The Assays by Design protocol was used for development of probes and primers for codon 136 and Primer Express for codon 171. Commercially available kits were used to isolate genomic DNA from blood or muscle. For validation, 70 SNP determinations for each codon were compared to commercial testing with an error rate of less than 1%. Then, 935 samples from blood (n = 818) and muscle (n = 117) were tested for both codons with 928 successful determinations and only 7 samples (<1% of total samples) that needed repeating. Genotypes were AA QQ (n = 102; 11.0%), AV QQ (n = 28; 3.0%), AA QR (n = 396; 42.7%), AV QR (n = 54; 5.8%), and AA RR (n = 348; 37.5%). Thus, 86% of the sheep tested (n = 798) contained R at codon 171 and were expected to be scrapie-resistant. This new Taqman 5' Nuclease SNP genotyping assay is accurate, easy to perform, and useful in the study of classical scrapie in sheep and its prevention through selective breeding programs to eliminate highly susceptible animals.     

Historical landscape ecology of an urbanized California valley: wetlands and woodlands in the Santa Clara Valley

Historical records provide information to land managers and landscape ecologists attempting to understand current trajectories in altered landscapes. In this study, we synthesized a heterogeneous array of historical sources to reconstruct historical land cover in California’s Santa Clara Valley (a.k.a. “Silicon Valley”). To increase and assess accuracy, we used the triangulation of overlapping, independent data sources and the application of certainty level standards. The region has been subject to extensive urbanization, so we also evaluated the applicability of historical landscape reconstructions to the altered landscape. We found evidence for five major land cover types prior to significant Euro–American modification. Valley freshwater marsh, wet meadow, alkali meadow, willow grove, and valley oak savanna have all experienced extreme decline (85–100%) since Euro–American settlement. However, comparison of historical land cover patterns to contemporary land use suggested several new strategies for environmental recovery, despite the limitations of surrounding urbanization. We also observed a temporal shift in riparian habitat along the mainstem of Coyote Creek, from a relatively open mixture of riparian scrub, sycamore woodland, and unvegetated gravel bars to dense riparian forest, likely resulting from stream flow regulation. By identifying former land cover patterns we provide a basis for evaluating local landscape change and setting restoration targets, including the identification of residual features and under-recognized land cover types. These findings suggest that reliable historical landscape reconstructions can be developed in the absence of standardized historical data sources and can be of value even in highly modified regions.     

Predicting the age of fish using general and generalized linear models of biometric data: A case study of two estuarine finfish from New South Wales, Australia

Direct ageing of fish can be a laborious and expensive task when age estimates from a large population are required, and often involves a degree of subjectivity. This study examined the application of general and generalized linear models that predict the age of fish from a range of efficiently and objectively measured covariates. The data sampled were from yellowfin bream (Acanthopagrus australis (Sparidae) (Owen, 1853)) and sand whiting (Sillago ciliata (Sillaginidae) Cuvier, 1829) populations from New South Wales, Australia. The covariates evaluated in the models were fish length, otolith weight, sex and location (the estuary from which the fish were sampled). Akaike Information Criteria were used for model selection and residual plots of the final models revealed a satisfactory fit to the observations. The best fitting model for each species included all covariates. An additional investigation considered whether general and generalized linear models that predict age from two different categories of biometric information outperform age-length keys with respect to subsequent estimates of total mortality from catch-curve analysis. The two categories of biometric information differed in the ease and cost with which the information could be collected. The first category only included fish length and location as covariates, whilst the second category also included otolith weight and sex. It was found that traditional age-length keys outperformed the predictive models that estimated age from only fish length and location, because the results from the models were prone to significant bias. However, when otolith weight and sex were added as covariates to the predictive models, some of them, including a generalized linear model with a Poisson-distributed response variable, performed similarly to the age-length key. Given that otolith weight and the sex of fish are cheaper to quantify than age from a sectioned otolith in many situations, general or generalized linear models may represent a cheaper and faster method of estimating mortality compared to age-length keys. Such models can also easily incorporate the influence of spatial, temporal and demographic variation.     

Association of brook trout and Oncorhynchus spp. with large wood jams in a Lake Superior tributary in a northern old‐growth watershed

Wood in streams functions as fish habitat, but relationships between fish abundance (or size) and large wood in streams are not consistent. One possible reason for variable relationships between fish and wood in streams is that the association of fish with wood habitat may depend on ecological context such as large‐scale geomorphology. We studied the relationship between salmonid assemblages and large wood jams (LWJ) in four settings that differed geomorphically at the scale of the stream corridor along a tributary to Lake Superior in old‐growth conifer–hardwood forest in northern Michigan. The focal fish species of this study were brook trout (Salvelinus fontinalis), which were wild in the stream. Relocation efforts for coaster brook trout (an adfluvial life history variant of brook trout) were ongoing in the study stream. We measured fish abundance and length in pairs of pools of similar size and substrate, but varying in the presence of LWJ; this allowed us to evaluate associations of fish simply with the presence of LWJ rather than with other channel or flow‐shaping functions of LWJ. The length of Oncorhynchus spp. and young introduced brook trout was not strongly correlated with LWJ presence; however, the presence of LWJ in pools was positively correlated with larger wild brook trout. We also found that the correspondence of LWJ with the abundance of salmonids appears to be moderated by the presence of alternative habitat in this relatively natural, old‐growth forest stream.     

Economic profitability of Nile tilapia (Oreochromis niloticus L.) production in Kenya

Economic profitability of Nile tilapia production in Kenya was analysed using a model that simulated individual fish growth and took fish population dynamics in the pond into account. The results suggest that the currently practiced mixed‐sex tilapia culture is economically unsustainable. It is suggested that research and extension efforts be geared towards developing monosex Nile tilapia production systems. Nile tilapia culture with African catfish predation should be viewed as an intermediate step towards all‐male Nile tilapia culture. This will allow accumulation of both physical and human capital to support all‐male tilapia culture. Under all‐male culture, economic returns are high enough to justify investment in Nile tilapia culture using borrowed capital. However, the success of monosex culture will depend on the availability and affordability of quality fingerlings and low‐cost fish feeds. The results have a wide application in Sub‐Saharan Africa where mixed‐sex Nile tilapia culture is common.     

A COMPARISON OF THE EFFECT OF ITALIAN RYEGRASS AND TALL FESCUE MIXTURES ON THE FOLLOWING CROPS OF KALE AND BARLEY

The effects of preeropping with Italian ryegrass and tall fescue mixtures on marrow-stem kale (1st test crop) and barley (2nd test crop) were measured. Application of N to the grass/clover swards reduced the yield of DM, P, K, Na, Mg, crude protein and also the percentage crude protein in the kale test-crop. Following the tall fescue swards, the yield of DM, P, Na, Ca, Mg and E, crude protein and percentage crude protein in the kale were lower than after the Italian ryegrass swards. These effects were particularly evident in the kale stem. Interactions occurred which involved the method used to establish the herbage mixtures, the application of N to the swards and of fertilizers to the kale. These effects were complex, but the method of sward establishment could clearly affect the following kale crop grown several years later. The influence of grass swards on the second test-crop (spring barley) was much smaller than on kale. Precropping with Italian ryegrass or using a cover crop during grassland establishment reduced 1000-grain weight of barley. The crude protein percentage in barley grain was reduced by the compound fertilizer applied to the previous kale crop, particularly when no cover crop had been used during establishment of the herbage mixtures. The converse of these effects was recorded in the crude-protein percentage of the straw of the barley test-crop.     

Live Transport of Striped Bass and Rainbow Trout Using a Hidrostal Pump

Immediate and delayed (96 h) mortality, descaling, and injury rates of striped bass Morone sax-atilis and rainbow trout Oncorhynchus mykiss that were inserted into the entrance (suction side) of a Hidrostal pump were compared to those of control fish that were inserted at the exit (pressure side). Comparisons were made in 158-paired trials of striped bass and 86 trials with rainbow trout. The Hidrostal pump had no significant effect on immediate or delayed (96 h) mortality. Immediate mortality for striped bass and rainbow trout averaged 0.1 and 0%, respectively, and delayed mortality averaged 2.9 and 0.1%, respectively. Mean scale loss after passage for striped bass and rainbow trout was low (0.2 and 1.0%, respectively). Frequency of injury to the head, eyes, skin, and tins of pumped striped bass averaged 1.9, 2.8, 1.9, and 18.7%, respectively, and those of rainbow trout averaged 2.3, 0, 2.4, and 3.1%. No significant relationships were detected between fish mortality and pump speed, injected fish density, and debris load. Results suggest that large Hidrostal pumps have the capacity to transport live striped bass and rainbow trout at high density (1-6 fish/L) with little mortality and body injury.