CAPTURE-RECAPTURE ESTIMATES OF HECTOR'S DOLPHIN ABUNDANCE AT BANKS PENINSULA, NEW ZEALAND

Capture-recapture techniques have been extensively used to estimate survival rates of Hector's dolphins at Banks Peninsula, but not abundance. We analyzed nine seasons of photo-identification data using a model-fitting approach in the computer program MARK, and then used MARK's estimates of capture probabilities to calculate the abundance of distinctive individuals. We extrapolated these estimates to include unmarked individuals using five seasons of data on the proportion of identifiable individuals in this population, obtained from "random photography." This capture-recapture approach suggests a 1996 population of about 1,100 (CV = 0.21). This is very similar to the 1997 line-transect estimate of about 900 (CV = 0.28), especially considering that the two techniques do not necessarily measure the same thing. An important advantage of the capture-recapture approach stems from the inherent versatility of photo-ID data. If the sampling design is appropriate, an unbiased abundance estimate can be achieved as a spin-off from work directed at other questions. However, in our view, line-transect estimates are easier to interpret because the sampling design is explicit.     

Population Estimation and Trappability of the European Badger (Meles meles): Implications for Tuberculosis Management

Estimates of population size and trappability inform vaccine efficacy modelling and are required for adaptive management during prolonged wildlife vaccination campaigns. We present an analysis of mark-recapture data from a badger vaccine (Bacille Calmette–Guérin) study in Ireland. This study is the largest scale (755 km²) mark-recapture study ever undertaken with this species. The study area was divided into three approximately equal–sized zones, each with similar survey and capture effort. A mean badger population size of 671 (SD: 76) was estimated using a closed-subpopulation model (CSpM) based on data from capturing sessions of the entire area and was consistent with a separate multiplicative model. Minimum number alive estimates calculated from the same data were on average 49–51% smaller than the CSpM estimates, but these are considered severely negatively biased when trappability is low. Population densities derived from the CSpM estimates were 0.82–1.06 badgers km⁻², and broadly consistent with previous reports for an adjacent area. Mean trappability was estimated to be 34–35% per session across the population. By the fifth capture session, 79% of the adult badgers caught had been marked previously. Multivariable modelling suggested significant differences in badger trappability depending on zone, season and age-class. There were more putatively trap-wary badgers identified in the population than trap-happy badgers, but wariness was not related to individual’s sex, zone or season of capture. Live-trapping efficacy can vary significantly amongst sites, seasons, age, or personality, hence monitoring of trappability is recommended as part of an adaptive management regime during large–scale wildlife vaccination programs to counter biases and to improve efficiencies.     

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community amplicon sequencing on the HiSeq2000 and MiSeq Illumina platforms, and apply that protocol to sequence 24 microbial communities from host-associated and free-living environments. A critical question as more sequencing platforms become available is whether biological conclusions derived on one platform are consistent with what would be derived on a different platform. We show that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the HiSeq2000 versus the MiSeq) and across the sequenced regions of amplicons.     

A genome wide association scan of bovine tuberculosis susceptibility in Holstein-Friesian dairy cattle

Background

Bovine tuberculosis is a significant veterinary and financial problem in many parts of the world. Although many factors influence infection and progression of the disease, there is a host genetic component and dissection of this may enlighten on the wider biology of host response to tuberculosis. However, a binary phenotype of presence/absence of infection presents a noisy signal for genomewide association study.

Methodology/Principal Findings

We calculated a composite phenotype of genetic merit for TB susceptibility based on disease incidence in daughters of elite sires used for artificial insemination in the Irish dairy herd. This robust measure was compared with 44,426 SNP genotypes in the most informative 307 subjects in a genome wide association analysis. Three SNPs in a 65 kb genomic region on BTA 22 were associated (i.e. p<10⁻⁵, peaking at position 59588069, p = 4.02×10⁻⁶) with tuberculosis susceptibility.

Conclusions/Significance

A genomic region on BTA 22 was suggestively associated with tuberculosis susceptibility; it contains the taurine transporter gene SLC6A6, or TauT, which is known to function in the immune system but has not previously been investigated for its role in tuberculosis infection.     

Plasma and urinary cytokine homeostasis and renal function during cardiac surgery without cardiopulmonary bypass

Cardiopulmonary bypass (CPB) significantly contributes to the plasma pro-inflammatory cytokine response at cardiac surgery. Complementary plasma and urinary anti-inflammatory cytokine responses have been described. The pro-inflammatory cytokines interleukin 8 (IL-8), tumour necrosis factor alpha (TNF-alpha) and interleukin 1beta (IL-1beta) have lower molecular weights than the anti-inflammatory cytokines interleukin 10 (IL-10), interleukin 1 receptor antagonist (IL-1ra) and TNF soluble receptor 2 (TNFsr2) and thus undergo glomerular filtration more readily. In vitro work suggests that proximal tubular cells are vulnerable to pro-inflammatory cytokine mediated injury. Accordingly, this study investigated the hypothesis that cardiac surgery without CPB would not have significant changes in plasma and urinary cytokines and proximal renal dysfunction. Eight patients undergoing coronary artery bypass grafting (CABG) without CPB were studied. Blood and urine samples were analysed for pro- and anti-inflammatory cytokines. Proximal tubular dysfunction was measured using urinary Nu-acetyl-beta-D-glucosaminidase (NAG)/creatinine and alpha(1)-microglobulin/creatinine ratios. Plasma IL-8, IL-10, IL-1ra and TNFsr2 were significantly elevated compared with baseline. Urinary IL-1ra and TNFsr2 were significantly elevated, as were urinary NAG/creatinine and alpha(1)-microglobulin/creatinine ratios. Two hours following revascularization, urinary IL-1ra correlated with urinary alpha(1)-microglobulin/creatinine ratios (P<0.05). As previously reported in CABG surgery with CPB, we now report that non-CPB cardiac surgery also has significant changes in plasma and urinary cytokine homeostasis and early proximal tubular injury. The correlation between urinary IL-1ra and alpha(1)-microglobulin/creatinine ratios is consistent with earlier suggestions of a mechanistic link between cytokine changes and proximal tubular dysfunction. The relative roles of CPB and non-CPB processes in producing inflammation still require definition.     

Molecular Detection of Mycobacterium bovis and Mycobacterium bovis BCG (Pasteur) in Soil

PCR primers specific for the Mycobacterium tuberculosis complex were used to detect the presence of Mycobacterium bovis BCG (Pasteur) in soil microcosms and Mycobacterium bovis in environmental samples taken from a farm in Ireland with a history of bovine tuberculosis. M. bovis genes were detected in soil at 4 and 21 months after possible contamination. Gene levels were found in the range of 1 × 10³ to 3.6 × 10³ gene copies g of soil⁻¹, depending on the sampling area. Areas around badger setts had the highest levels of detectable genes and were shown to have the highest levels of gene persistence. M. bovis-specific 16S rRNA sequences were detected, providing evidence of the presence of viable cells in Irish soils. Studies of DNA turnover in soil microcosms proved that dead cells of M. bovis BCG did not persist beyond 10 days. Further microcosm experiments revealed that M. bovis BCG survival was optimal at 37°C with moist soil (−20 kPa; 30% [vol/wt]). This study provides clear evidence that M. bovis can persist in the farm environment outside of its hosts and that climatic factors influence survival rates.     

Phylogenetic diversity of stress signalling pathways in fungi

Background  

Microbes must sense environmental stresses, transduce these signals and mount protective responses to survive in hostile environments. In this study we have tested the hypothesis that fungal stress signalling pathways have evolved rapidly in a niche-specific fashion that is independent of phylogeny. To test this hypothesis we have compared the conservation of stress signalling molecules in diverse fungal species with their stress resistance. These fungi, which include ascomycetes, basidiomycetes and microsporidia, occupy highly divergent niches from saline environments to plant or mammalian hosts.     

An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

Background  

Tunicates have been recently revealed to be the closest living relatives of vertebrates. Yet, with more than 2500 described species, details of their evolutionary history are still obscure. From a molecular point of view, tunicate phylogenetic relationships have been mostly studied based on analyses of 18S rRNA sequences, which indicate several major clades at odds with the traditional class-level arrangements. Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups such as the Aplousobranchia, Appendicularia, and Thaliacea.