Transcriptional profiling of the bovine hepatic response to experimentally induced E. coli mastitis.

The mammalian liver works to keep the body in a state of homeostasis and plays an important role in systemic acute phase response to infections. In this study we investigated the bovine hepatic acute phase response at the gene transcription level in dairy cows with experimentally Escherichia coli-induced mastitis. At time = 0, each of 16 periparturient dairy cows received 20-40 colony-forming units of live E. coli in one front quarter of the udder. A time series of liver biopsies was collected at -144, 12, 24, and 192 h relative to time of inoculation. Changes in transcription levels in response to E. coli inoculation were analyzed using the Bovine Genome Array and tested significant for 408 transcripts over the time series [adjusted p ≤ 0.05, abs(fold-change) > 2]. After 2-D clustering, transcripts represented three distinct transcription profiles: 1) regulation of gene transcription and apoptosis, 2) responses to cellular stress invoked by reactive metabolites, and 3) metabolism and turnover of proteins. The results showed that the liver went through a period of perturbations to its normal homeostatic condition during the first 24 h following the E. coli-induced intra-mammary inflammation. In previous studies, bacterial lipopolysaccharide, LPS, was used for intramammary stimulation to mimic E. coli infection. Comparing responses to LPS and E. coli, induced biochemical processes were similar but not identical (94 and 85% similarity between corresponding samples at early and late acute phase, respectively), but their kinetics were not. A notable difference concerned transcription of factors associated with oxidative stress in E. coli-induced liver responses.

Assembling a dual purpose TaqMan-based panel of single-nucleotide polymorphism markers in rainbow trout and steelhead (Oncorhynchus mykiss) for association mapping and population genetics analysis.

We establish a TaqMan-based assay panel for genotyping single-nucleotide polymorphisms in rainbow trout and steelhead (Oncorhynchus mykiss). We develop 22 novel single-nucleotide polymorphism markers based on new steelhead sequence data and on assays from sister taxa. Additionally, we adapt 154 previously developed markers to the TaqMan platform. At the beginning of this study, 59 SNPs with TaqMan assays were available to the scientific community. By adding 176 additional TaqMan assays to this number, we greatly expand the biological applications of TaqMan genotyping within both population genetics and quantitative genetics.

Disentangling the effects of evolutionary, demographic, and environmental factors influencing genetic structure of natural populations: Atlantic herring as a case study.

The spatial structuring of intraspecific genetic diversity is the result of random genetic drift, natural selection, migration, mutation, and their interaction with historical processes. The contribution of each has been typically difficult to estimate, but recent advances in statistical genetics have provided valuable new investigative tools to tackle such complexity. Using a combination of such methods, we examined the roles of environment (i.e., natural selection), random genetic processes (i.e., drift), and demography and life histories (e.g., feeding migrations) on population structure of a widely distributed and abundant marine pelagic fish of economic importance, Atlantic herring (Clupea harengus). Individuals were collected during peak spawning time from 19 spawning locations spanning the region from the western North Sea to the eastern Baltic Sea (N= 1859, eight microsatellite loci). We carried out separate analyses of neutral and selected genetic variation, which allowed us to establish that the two most important factors affecting population structure were selection due to salinity at spawning sites and feeding migrations. The genetic signal left by the demographic history of herring, on the other hand, seems to have been largely eroded, which is not surprising given the large reproductive potential and presumed enormous local effective population sizes of pelagic fish that constrain the effect of stochastic processes. The approach we used can in principle be applied to any abundant and widely distributed aquatic or terrestrial species.

Marine landscapes and population genetic structure of herring (Clupea harengus L.) in the Baltic Sea.

Numerically small but statistically significant genetic differentiation has been found in many marine fish species despite very large census population sizes and absence of obvious barriers to migrating individuals. Analyses of morphological traits have previously identified local spawning groups of herring (Clupea harengus L.) in the environmentally heterogeneous Baltic Sea, whereas allozyme markers have not revealed differentiation. We analysed variation at nine microsatellite loci in 24 samples of spring-spawning herring collected at 11 spawning locations throughout the Baltic Sea. Significant temporal differentiation was observed at two locations, which we ascribe to sympatrically spawning but genetically divergent 'spawning waves'. Significant differentiation was also present on a geographical scale, though pairwise F(ST) values were generally low, not exceeding 0.027. Partial Mantel tests showed no isolation by geographical distance, but significant associations were observed between genetic differentiation and environmental parameters (salinity and surface temperature) (0.001 < P < or = 0.099), though these outcomes were driven mainly by populations in the southwestern Baltic Sea, which also exhibits the steepest environmental gradients. Application of a novel method for detecting barriers to gene flow by combining geographical coordinates and genetic differentiation allowed us to identify two zones of lowered gene flow. These zones were concordant with the separation of the Baltic Sea into major basins, with environmental gradients and with differences in migration behaviour. We suggest that similar use of landscape genetics approaches may increase the understanding of the biological significance of genetic differentiation in other marine fishes.