Using molecular markers with high mutation rates to obtain estimates of relative population size and to distinguish the effects of gene flow and mutation: a demonstration using data from endemic Mauritian skinks

We propose a method of analysing genetic data to obtain separate estimates of the size (N(p)) and migration rate (m(p)) for the sampled populations, without precise prior knowledge of mutation rates at each locus ( micro(L)). The effects of migration and mutation can be distinguished because high migration has the effect of reducing genetic differentiation across all loci, whereas a high mutation rate will only affect the locus in question. The method also takes account of any differences between the spectra of immigrant alleles and of new mutant alleles. If the genetic data come from a range of population sizes, and the loci have a range of mutation rates, it is possible to estimate the relative sizes of the different N(p) values, and likewise the m(p) and the micro(L). Microsatellite loci may also be particularly appropriate because loci with a high mutation rate can reach mutation-drift-migration equilibrium more quickly, and because the spectra of mutants arriving in a population can be particularly distinct from the immigrants. We demonstrate this principle using a microsatellite data set from Mauritian skinks. The method identifies low gene flow between a putative new species and populations of its sister species, whereas the differentiation of two other populations is attributed to small population size. These distinct interpretations were not readily apparent from conventional measures of genetic differentiation and gene diversity. When the method is evaluated using simulated data sets, it correctly distinguishes low gene flow from small population size. Loci that are not at mutation-migration-drift equilibrium can distort the parameter estimates slightly. We discuss strategies for detecting and overcoming this effect.     

The Use of Nanotrap Particles in the Enhanced Detection of Rift Valley Fever Virus Nucleoprotein

BackgroundRift Valley fever virus (RVFV) is a highly pathogenic arthropod-borne virus that has a detrimental effect on both livestock and human populations. While there are several diagnostic methodologies available for RVFV detection, many are not sensitive enough to diagnose early infections. Furthermore, detection may be hindered by high abundant proteins such as albumin. Previous findings have shown that Nanotrap particles can be used to significantly enhance detection of various small analytes of low abundance. We have expanded upon this repertoire to show that this simple and efficient sample preparation technology can drastically improve the detection of the RVFV nucleoprotein (NP), the most abundant and widely used viral protein for RVFV diagnostics.ResultsAfter screening multiple Nanotrap particle architectures, we found that one particle, NT45, was optimal for RVFV NP capture, as demonstrated by western blotting. NT45 significantly enhanced detection of the NP at levels undetectable without the technology. Importantly, we demonstrated that Nanotrap particles are capable of concentrating NP in a number of matrices, including infected cell lysates, viral supernatants, and animal sera. Specifically, NT45 enhanced detection of NP at various viral titers, multiplicity of infections, and time points. Our most dramatic results were observed in spiked serum samples, where high abundance serum proteins hindered detection of NP without Nanotrap particles. Nanotrap particles allowed for sample cleanup and subsequent detection of RVFV NP. Finally, we demonstrated that incubation of our samples with Nanotrap particles protects the NP from degradation over extended periods of time (up to 120 hours) and at elevated temperatures (at 37ºC).ConclusionThis study demonstrates that Nanotrap particles are capable of drastically lowering the limit of detection for RVFV NP by capturing, concentrating, and preserving RVFV NP in clinically relevant matrices. These studies can be extended to a wide range of pathogens and their analytes of diagnostic interest.     

Moving forward with the primate microbiome: Introduction to a special issue of the American Journal of Primatology

Primate microbiome research is a quickly growing field with exciting potential for informing our understanding of primate biology, ecology, and evolution as well as host‐microbe interactions more broadly. This introductory essay to a special section of the American Journal of Primatology provides a cross‐sectional snapshot of current activity in these areas by briefly summarizing the diversity of contributed papers and their relationships to key themes in host‐associated microbiome research. It then uses this survey as a foundation for consolidating a set of key research questions to broadly guide future research. It also argues for the importance of methods standardization to facilitate comparative analyses and the identification of generalizable patterns and relationships. While primatology will benefit greatly from the integration of microbial datasets, it is uniquely positioned to address important questions regarding microbiology and macro‐ecology and evolution more generally. We are eager to see where the primate microbiome leads us.     

Alternative methods for disposal of spent laying hens: Evaluation of the efficacy of grinding,mechanical deboning,and of keratinase in the rendering process

Besides the challenges of mortality and litter disposal, the poultry industry must find economical means of disposing of laying hens that have outlived their productive lives. Because spent hens have low market value and disposing of them by composting and burial is often infeasible, finding alternative disposal methods that are environmentally secure is prudent. The feasibility of grinding or mechanically deboning spent hens with and without prior mechanical picking was evaluated for the production of various proteinaceous by-product meals. The end products were analyzed for nutrient content and found to be high in protein (35.3–91.9% CP) and, with the exception of the feathers, high in fat (24.1–58.3%), making them potentially valuable protein and energy sources. After considering physical and economic feasibility, mechanical deboning was determined to be a logical first step for the conversion of spent hens into value-added by-product meals. Because the hard tissue fraction (primarily feathers, bones, and connective tissue) generated by mechanically deboning the hens presents the greatest challenge to their utilization as feedstuffs, attention was focused on technologies that could potentially improve the nutritional value of the hard tissue for use as a ruminant protein source. Traditional hydrolysis of this hard tissue fraction improved its pepsin digestibility from 74% to 85%; however, subsequent keratinase enzyme treatment for 1 h, 2 h, 4 h, or 20 h after steam hydrolysis failed to improve the pepsin or amino acid digestibility any further (P > 0.10). Enzyme hydrolysis did, however, increase the quantities of the more soluble protein fractions (A: 45.5, 46.6, 52.8, 51.6, and 55.8% of CP; B₁: 3.2, 9.8, 6.0, 4.6, and 4.1% of CP; B₂: 11.7, 18.1, 22.8, 29.6, and 22.0% of CP for 0, 1 h, 2 h, 4 h, and 20 h, respectively) and reduced quantities of the less soluble fractions (B₃: 30.2, 18.1, 10.8, 5.5, and 10.2% of CP; C: 9.4, 7.5, 7.6, 8.8, and 7.9% of CP for 0, 1 h, 2 h, 4 h, and 20 h, respectively). The protein digestibility of the steam hydrolyzed hard tissue fraction from the mechanical deboning of spent hens was found to be comparable to the digestibility of feather meal, but post-hydrolysis keratinase treatment did not improve feeding value for ruminants.     

The ontogeny of flehmen in horses

Flehmen behaviour in Welsh pony (Equus caballus) mares and foals living on pasture was observed during 807 h of focal sampling. A series of flehmens performed at one site was defined as a flehmen incident. Colts exhibited flehmen incidents and performed flehmen more frequently during an incident than did fillies or mares. Filies exhibited flehmen incidents more frequently than did mares, but did not flehmen more frequently during an incident. Colts exhibited a peak frequency of performing flehmen and of flehmen incidents during weeks 1–4 with a subsequent linear decrease in frequency up to weeks 17–20. Usually, flehmen occurred without the subject having had direct contact of the nostrils, lips, or tongue with a possible stimulant. Twenty-six per cent of the flehmen incidents occurred during or after urination by another pony. Seven per cent of the incidents occurred during or after urination by the pony showing flehmen.