2,372 research outputs found
2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador
Background:
Rhodnius ecuadoriensis is the main triatomine vector of Chagas disease, American trypanosomiasis, in Southern Ecuador and Northern Peru. Genomic approaches and next generation sequencing technologies have become powerful tools for investigating population diversity and structure which is a key consideration for vector control. Here we assess the effectiveness of three different 2b restriction site-associated DNA (2b-RAD) genotyping strategies in R. ecuadoriensis to provide sufficient genomic resolution to tease apart microevolutionary processes and undertake some pilot population genomic analyses.
Methodology/Principal findings:
The 2b-RAD protocol was carried out in-house at a non-specialized laboratory using 20 R. ecuadoriensis adults collected from the central coast and southern Andean region of Ecuador, from June 2006 to July 2013. 2b-RAD sequencing data was performed on an Illumina MiSeq instrument and analyzed with the STACKS de novo pipeline for loci assembly and Single Nucleotide Polymorphism (SNP) discovery. Preliminary population genomic analyses (global AMOVA and Bayesian clustering) were implemented. Our results showed that the 2b-RAD genotyping protocol is effective for R. ecuadoriensis and likely for other triatomine species. However, only BcgI and CspCI restriction enzymes provided a number of markers suitable for population genomic analysis at the read depth we generated. Our preliminary genomic analyses detected a signal of genetic structuring across the study area.
Conclusions/Significance:
Our findings suggest that 2b-RAD genotyping is both a cost effective and methodologically simple approach for generating high resolution genomic data for Chagas disease vectors with the power to distinguish between different vector populations at epidemiologically relevant scales. As such, 2b-RAD represents a powerful tool in the hands of medical entomologists with limited access to specialized molecular biological equipment.
Author summary:
Understanding Chagas disease vector (triatomine) population dispersal is key for the design of control measures tailored for the epidemiological situation of a particular region. In Ecuador, Rhodnius ecuadoriensis is a cause of concern for Chagas disease transmission, since it is widely distributed from the central coast to southern Ecuador. Here, a genome-wide sequencing (2b-RAD) approach was performed in 20 specimens from four communities from Manabí (central coast) and Loja (southern) provinces of Ecuador, and the effectiveness of three type IIB restriction enzymes was assessed. The findings of this study show that this genotyping methodology is cost effective in R. ecuadoriensis and likely in other triatomine species. In addition, preliminary population genomic analysis results detected a signal of population structure among geographically distinct communities and genetic variability within communities. As such, 2b-RAD shows significant promise as a relatively low-tech solution for determination of vector population genomics, dynamics, and spread
Search for very-high-energy emission from Gamma-ray Bursts using the first 18 months of data from the HAWC Gamma-ray Observatory
The High Altitude Water Cherenkov (HAWC) Gamma-ray Observatory is an
extensive air shower detector operating in central Mexico, which has recently
completed its first two years of full operations. If for a burst like GRB
130427A at a redshift of 0.34 and a high-energy component following a power law
with index -1.66, the high-energy component is extended to higher energies with
no cut-off other than from extragalactic background light attenuation, HAWC
would observe gamma rays with a peak energy of 300 GeV. This paper
reports the results of HAWC observations of 64 gamma-ray bursts (GRBs) detected
by and , including three GRBs that were also
detected by the Large Area Telescope (-LAT). An ON/OFF analysis
method is employed, searching on the time scale given by the observed light
curve at keV-MeV energies and also on extended time scales. For all GRBs and
time scales, no statistically significant excess of counts is found and upper
limits on the number of gamma rays and the gamma-ray flux are calculated. GRB
170206A, the third brightest short GRB detected by the Gamma-ray Burst Monitor
on board the satellite (-GBM) and also
detected by the LAT, occurred very close to zenith. The LAT measurements can
neither exclude the presence of a synchrotron self-Compton (SSC) component nor
constrain its spectrum. Instead, the HAWC upper limits constrain the expected
cut-off in an additional high-energy component to be less than
for reasonable assumptions about the energetics and redshift of the burst.Comment: 19 pages, 6 figures, published in Ap
Seroprevalence and risk factors for Q-fever (Coxiella burnetii) exposure in smallholder dairy cattle in Tanzania
Q fever is a zoonotic disease, resulting from infection with Coxiella burnetii. Infection in cattle can cause abortion and infertility, however, there is little epidemiological information regarding the disease in dairy cattle in Tanzania. Between July 2019 and October 2020, a serosurvey was conducted in six high dairy producing regions of Tanzania. Cattle sera were tested for antibodies to C. burnetii using an indirect enzyme-linked immunosorbent assay. A mixed effect logistic regression model identified risk factors associated with C. burnetii seropositivity. A total of 79 out of 2049 dairy cattle tested positive with an overall seroprevalence of 3.9% (95% CI 3.06–4.78) across the six regions with the highest seroprevalence in Tanga region (8.21%, 95% CI 6.0–10.89). Risk factors associated with seropositivity included: extensive feeding management (OR 2.77, 95% CI 1.25–3.77), and low precipitation below 1000 mm (OR 2.76, 95% 1.37–7.21). The disease seroprevalence is relatively low in the high dairy cattle producing regions of Tanzania. Due to the zoonotic potential of the disease, future efforts should employ a “One Health” approach to understand the epidemiology, and for interdisciplinary control to reduce the impacts on animal and human health
All-particle cosmic ray energy spectrum measured by the HAWC experiment from 10 to 500 TeV
We report on the measurement of the all-particle cosmic ray energy spectrum
with the High Altitude Water Cherenkov (HAWC) Observatory in the energy range
10 to 500 TeV. HAWC is a ground based air-shower array deployed on the slopes
of Volcan Sierra Negra in the state of Puebla, Mexico, and is sensitive to
gamma rays and cosmic rays at TeV energies. The data used in this work were
taken from 234 days between June 2016 to February 2017. The primary cosmic-ray
energy is determined with a maximum likelihood approach using the particle
density as a function of distance to the shower core. Introducing quality cuts
to isolate events with shower cores landing on the array, the reconstructed
energy distribution is unfolded iteratively. The measured all-particle spectrum
is consistent with a broken power law with an index of prior to
a break at ) TeV, followed by an index of . The
spectrum also respresents a single measurement that spans the energy range
between direct detection and ground based experiments. As a verification of the
detector response, the energy scale and angular resolution are validated by
observation of the cosmic ray Moon shadow's dependence on energy.Comment: 16 pages, 11 figures, 4 tables, submission to Physical Review
Constraining the Ratio in TeV Cosmic Rays with Observations of the Moon Shadow by HAWC
An indirect measurement of the antiproton flux in cosmic rays is possible as
the particles undergo deflection by the geomagnetic field. This effect can be
measured by studying the deficit in the flux, or shadow, created by the Moon as
it absorbs cosmic rays that are headed towards the Earth. The shadow is
displaced from the actual position of the Moon due to geomagnetic deflection,
which is a function of the energy and charge of the cosmic rays. The
displacement provides a natural tool for momentum/charge discrimination that
can be used to study the composition of cosmic rays. Using 33 months of data
comprising more than 80 billion cosmic rays measured by the High Altitude Water
Cherenkov (HAWC) observatory, we have analyzed the Moon shadow to search for
TeV antiprotons in cosmic rays. We present our first upper limits on the
fraction, which in the absence of any direct measurements, provide
the tightest available constraints of on the antiproton fraction for
energies between 1 and 10 TeV.Comment: 10 pages, 5 figures. Accepted by Physical Review
Measurement of the Crab Nebula Spectrum Past 100 TeV with HAWC
We present TeV gamma-ray observations of the Crab Nebula, the standard
reference source in ground-based gamma-ray astronomy, using data from the High
Altitude Water Cherenkov (HAWC) Gamma-Ray Observatory. In this analysis we use
two independent energy-estimation methods that utilize extensive air shower
variables such as the core position, shower angle, and shower lateral energy
distribution. In contrast, the previously published HAWC energy spectrum
roughly estimated the shower energy with only the number of photomultipliers
triggered. This new methodology yields a much improved energy resolution over
the previous analysis and extends HAWC's ability to accurately measure
gamma-ray energies well beyond 100 TeV. The energy spectrum of the Crab Nebula
is well fit to a log parabola shape with emission up to at least 100 TeV. For the first
estimator, a ground parameter that utilizes fits to the lateral distribution
function to measure the charge density 40 meters from the shower axis, the
best-fit values are
=(2.350.04)10 (TeV cm
s), =2.790.02, and
=0.100.01. For the second estimator, a neural
network which uses the charge distribution in annuli around the core and other
variables, these values are
=(2.310.02)10 (TeV cm
s), =2.730.02, and
=0.060.010.02. The first set of uncertainties are statistical;
the second set are systematic. Both methods yield compatible results. These
measurements are the highest-energy observation of a gamma-ray source to date.Comment: published in Ap
- …