Reliable microsatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA

The potential link between badgers and bovine tuberculosis has made it vital to develop accurate techniques to census badgers. Here we investigate the potential of using genetic profiles obtained from faecal DNA as a basis for population size estimation. After trialling several methods we obtained a high amplification success rate (89%) by storing faeces in 70% ethanol and using the guanidine thiocyanate/silica method for extraction. Using 70% ethanol as a storage agent had the advantage of it being an antiseptic. In order to obtain reliable genotypes with fewer amplification reactions than the standard multiple-tubes approach, we devised a comparative approach in which genetic profiles were compared and replication directed at similar, but not identical, genotypes. This modified method achieved a reduction in polymerase chain reactions comparable with the maximumlikelihood model when just using reliability criteria, and was slightly better when using reliability criteria with the additional proviso that alleles must be observed twice to be considered reliable. Our comparative approach would be best suited for studies that include multiple faeces from each individual. We utilized our approach in a well-studied population of badgers from which individuals had been sampled and reliable genotypes obtained. In a study of 53 faeces sampled from three social groups over 10 days, we found that direct enumeration could not be used to estimate population size, but that the application of mark–recapture models has the potential to provide more accurate results

Estimation of capture probabilities using generalized estimating equations and mixed effects approaches

Modeling individual heterogeneity in capture probabilities has been one of the most challenging tasks in capture-recapture studies. Heterogeneity in capture probabilities can be modeled as a function of individual covariates, but correlation structure among capture occasions should be taking into account. A proposed generalized estimating equations (GEE) and generalized linear mixed modeling (GLMM) approaches can be used to estimate capture probabilities and population size for capture-recapture closed population models. An example is used for an illustrative application and for comparison with currently used methodology. A simulation study is also conducted to show the performance of the estimation procedures. Our simulation results show that the proposed quasi-likelihood based on GEE approach provides lower SE than partial likelihood based on either generalized linear models (GLM) or GLMM approaches for estimating population size in a closed capture-recapture experiment. Estimator performance is good if a large proportion of individuals are captured. For cases where only a small proportion of individuals are captured, the estimates become unstable, but the GEE approach outperforms the other methods

Multivariate morphometric analysis of Apis cerana of southern mainland Asia

Multivariate morphometric analyses were performed on a series of worker honeybees, Apis cerana, representing 557 colonies from all of southern mainland Asia extending from Afghanistan to Vietnam south of the Himalayas. Scores from the principal components analysis revealed five statistically separable but not entirely distinct morphoclusters of bees: (1) the Hindu Kush, Kashmir, N. Myanmar, N. Vietnam and S. China; (2) Himachal Pradesh region of N. India; (3) N. India, Nepal; (4) central and S. Myanmar and Vietnam, Cambodia, Thailand, S. China and peninsular Malaysia; (5) central and S. India. The major morphoclusters are distributed coherently with the different climatic zones of the region. While populations are definable, nomenclatural adjustments remain for the future

Search for the lepton-family-number nonconserving decay \mu -> e + \gamma

The MEGA experiment, which searched for the muon- and electron-number violating decay \mu -> e + \gamma, is described. The spectrometer system, the calibrations, the data taking procedures, the data analysis, and the sensitivity of the experiment are discussed. The most stringent upper limit on the branching ratio of \mu -> e + \gamma) < 1.2 x 10^{-11} was obtained

Rabies Management Implications Based on Raccoon Population Density Indexes

An estimate or index of target species density is important in determining oral rabies vaccination (ORV) bait densities to control and eliminate specific rabies variants. From 1997–2011, we indexed raccoon (Procyon lotor) densities 253 times based on cumulative captures on 163 sites from Maine to Alabama, USA, near ORV zones created to prevent raccoon rabies from spreading to new areas. We conducted indexing under a common cage trapping protocol near the time of annual ORV to aid in bait density decisions. Unique raccoons (n = 8,415) accounted for 68.0% of captures (n = 12,367). We recaptured raccoons 2,669 times. We applied Schnabel and Huggins mark‐recapture models on sites with ≥3 years of capture data and ≥25% recaptures as context for raccoon density indexes (RDIs). Simple linear relationships between RDIs and mark‐recapture estimates supported application of our 2 index. Raccoon density indexes ranged from 0.0–56.9 raccoons/km . For bait density decisions, we evaluated RDIs in the following 4 raccoon density groups, which were statistically different: (0.0–5.0 [n = 70], 5.1–15.0 [n = 129], 15.1–25.0 [n = 31], and \u3e25.0 raccoons/km2 [n = 23]). Mean RDI was positively associated with a higher percentage of developed land cover and a lower percentage of evergreen forest. Non‐target species composition (excluding recaptured raccoons) accounted for 32.0% of captures. Potential bait competitors accounted for 76.5% of non‐targets. The opossum (Didelphis virginiana) was the primary potential bait competitor from 27°N to 44°N latitude, north of which it was numerically replaced by the striped skunk (Mephitis mephitis). We selected the RDI approach over mark-recapture methods because of costs, geographic scope, staff availability, and the need for supplemental serologic samples. The 4 density groups provided adequate sensitivity to support bait density decisions for the current 2 bait density options. Future improvements to the method include providing random trapping locations to field personnel to prevent trap clustering and marking non‐targets to better characterize bait competitors

Time-resolved temperature measurements during pulsed laser irradiation uslng thin film metal thermometers

In this article, we describe a technique using Nisi and Pt thin film metal thermometers to provide accurate temperature information on a nanosecond time scale during pulsed laser processing of materials. A surface layer of interest is deposited onto the thermometer layer, and temperatures are determined from temperature dependent changes in the metal film&apos;s resistance. Details concerning the design and fabrication of the device structure and experimental considerations in making nanosecond resolved resistance measurements are discussed. Simple analytical estimates are presented to extract quantities such as incident laser energy stored in the sample. Finally, transient temperature data in the thermometer film, in combination with heat flow calculations, allow temperature determination as a function of time and depth into the sample and, additionally, can provide information about material properties of the surface layer

Enrichment of CpG island shore region hypermethylation in epigenetic breast field cancerization

While changes in DNA methylation are known to occur early in breast carcinogenesis and the landscape of breast tumour DNA methylation is profoundly altered compared with normal tissue, there have been limited efforts to identify DNA methylation field cancerization effects in histologically normal breast tissue adjacent to tumour. Matched tumour, histologically normal tissue of the ipsilateral breast (ipsilateral-normal), and histologically normal tissue of the contralateral breast (contralateral-normal) were obtained from nine women undergoing bilateral mastectomy. Laser capture microdissection was used to select epithelial cells from normal tissue, and neoplastic cells from tumour for genome-scale measures of DNA methylation with the Illumina HumanMethylationEPIC array. We identified substantially more CpG loci that were differentially methylated between contralateral-normal and tumour (63,271 CpG loci q \u3c 0.01), than between ipsilateral-normal and tumour (38,346 CpG loci q \u3c 0.01). We identified differential methylation in ipsilateral-normal relative to contralateral-normal tissue (9,562 CpG loci p \u3c 0.01). In this comparison, hypomethylated loci were significantly enriched for breast cancer-relevant transcription factor binding sites including those for ESR1, FoxA1, and GATA3 and hypermethylated loci were significantly enriched for CpG island shore regions. In addition, progression of shore hypermethylation was observed in tumours compared to matched ipsilateral normal tissue, and these alterations tracked to several well-established tumour suppressor genes. Our results indicate an epigenetic field effect in surrounding histologically normal tissue. This work offers an opportunity to focus investigations of early DNA methylation alterations in breast carcinogenesis and potentially develop epigenetic biomarkers of disease risk

Solar neutrino with Borexino: results and perspectives

Borexino is a unique detector able to perform measurement of solar neutrinos fluxes in the energy region around 1 MeV or below due to its low level of radioactive background. It was constructed at the LNGS underground laboratory with a goal of solar $^{7}$Be neutrino flux measurement with 5\% precision. The goal has been successfully achieved marking the end of the first stage of the experiment. A number of other important measurements of solar neutrino fluxes have been performed during the first stage. Recently the collaboration conducted successful liquid scintillator repurification campaign aiming to reduce main contaminants in the sub-MeV energy range. With the new levels of radiopurity Borexino can improve existing and challenge a number of new measurements including: improvement of the results on the Solar and terrestrial neutrino fluxes measurements; measurement of pp and CNO solar neutrino fluxes; search for non-standard interactions of neutrino; study of the neutrino oscillations on the short baseline with an artificial neutrino source (search for sterile neutrino) in context of SOX project.Comment: 15 pages, 4 figure

Recent Borexino results and prospects for the near future

The Borexino experiment, located in the Gran Sasso National Laboratory, is an organic liquid scintillator detector conceived for the real time spectroscopy of low energy solar neutrinos. The data taking campaign phase I (2007 - 2010) has allowed the first independent measurements of 7Be, 8B and pep fluxes as well as the first measurement of anti-neutrinos from the earth. After a purification of the scintillator, Borexino is now in phase II since 2011. We review here the recent results achieved during 2013, concerning the seasonal modulation in the 7Be signal, the study of cosmogenic backgrounds and the updated measurement of geo-neutrinos. We also review the upcoming measurements from phase II data (pp, pep, CNO) and the project SOX devoted to the study of sterile neutrinos via the use of a 51Cr neutrino source and a 144Ce-144Pr antineutrino source placed in close proximity of the active material.Comment: 8 pages, 11 figures. To be published as proceedings of Rencontres de Moriond EW 201

Search for Solar Axions Produced in p(d,3He)Ap(d,\rm{^3He})A Reaction with Borexino Detector

A search for 5.5-MeV solar axions produced in the $p+d\rightarrow\rm{^3He}+A (5.5 \rm{MeV})$ reaction was performed using the Borexino detector. The Compton conversion of axions to photons, ${\rm A}+e\rightarrow e+\gamma$; the axio-electric effect, ${\rm A}+e+Z\rightarrow e+Z$; the decay of axions into two photons, ${\rm A}\rightarrow2\gamma$; and inverse Primakoff conversion on nuclei, ${\rm A}+Z\rightarrow\gamma+Z$, are considered. Model independent limits on axion-electron ($g_{Ae}$), axion-photon ($g_{A\gamma}$), and isovector axion-nucleon ($g_{3AN}$) couplings are obtained: $|g_{Ae}\times g_{3AN}| \leq 5.5\times 10^{-13}$ and $|g_{A\gamma}\times g_{3AN}| \leq 4.6\times 10^{-11} \rm{GeV}^{-1}$ at $m_A <$ 1 MeV (90% c.l.). These limits are 2-4 orders of magnitude stronger than those obtained in previous laboratory-based experiments using nuclear reactors and accelerators.Comment: 11 pages, 7 figures, submitted to Phys.Rev.