A BAC-based physical map of the Hessian fly genome anchored to polytene chromosomes

<p>Abstract</p> <p>Background</p> <p>The Hessian fly (<it>Mayetiola destructor</it>) is an important insect pest of wheat. It has tractable genetics, polytene chromosomes, and a small genome (158 Mb). Investigation of the Hessian fly presents excellent opportunities to study plant-insect interactions and the molecular mechanisms underlying genome imprinting and chromosome elimination. A physical map is needed to improve the ability to perform both positional cloning and comparative genomic analyses with the fully sequenced genomes of other dipteran species.</p> <p>Results</p> <p>An FPC-based genome wide physical map of the Hessian fly was constructed and anchored to the insect's polytene chromosomes. Bacterial artificial chromosome (BAC) clones corresponding to 12-fold coverage of the Hessian fly genome were fingerprinted, using high information content fingerprinting (HIFC) methodology, and end-sequenced. Fluorescence <it>in situ </it>hybridization (FISH) co-localized two BAC clones from each of the 196 longest contigs on the polytene chromosomes. An additional 70 contigs were positioned using a single FISH probe. The 266 FISH mapped contigs were evenly distributed and covered 60% of the genome (95,668 kb). The ends of the fingerprinted BACs were then sequenced to develop the capacity to create sequenced tagged site (STS) markers on the BACs in the map. Only 3.64% of the BAC-end sequence was composed of transposable elements, helicases, ribosomal repeats, simple sequence repeats, and sequences of low complexity. A relatively large fraction (14.27%) of the BES was comprised of multi-copy gene sequences. Nearly 1% of the end sequence was composed of simple sequence repeats (SSRs).</p> <p>Conclusion</p> <p>This physical map provides the foundation for high-resolution genetic mapping, map-based cloning, and assembly of complete genome sequencing data. The results indicate that restriction fragment length heterogeneity in BAC libraries used to construct physical maps lower the length and the depth of the contigs, but is not an absolute barrier to the successful application of the technology. This map will serve as a genomic resource for accelerating gene discovery, genome sequencing, and the assembly of BAC sequences. The Hessian fly BAC-clone assembly, and the names and positions of the BAC clones used in the FISH experiments are publically available at <url>http://genome.purdue.edu/WebAGCoL/Hfly/WebFPC/</url>.</p

Search for the Neutron Decay n→\rightarrow X+γ\gamma where X is a dark matter particle

In a recent paper submitted to Physical Review Letters, Fornal and Grinstein have suggested that the discrepancy between two different methods of neutron lifetime measurements, the beam and bottle methods can be explained by a previously unobserved dark matter decay mode, n$\rightarrow$ X+$\gamma$ where X is a dark matter particle. We have performed a search for this decay mode over the allowed range of energies of the monoenergetic gamma ray for X to be a dark matter particle. We exclude the possibility of a sufficiently strong branch to explain the lifetime discrepancy with greater than 4 sigma confidence.Comment: 6 pages 3 figure

Measurement of the neutron lifetime using an asymmetric magneto- gravitational trap and in situ detection

The precise value of the mean neutron lifetime, $\tau_n$, plays an important role in nuclear and particle physics and cosmology. It is a key input for predicting the ratio of protons to helium atoms in the primordial universe and is used to search for new physics beyond the Standard Model of particle physics. There is a 3.9 standard deviation discrepancy between $\tau_n$ measured by counting the decay rate of free neutrons in a beam (887.7 $\pm$ 2.2 s) and by counting surviving ultracold neutrons stored for different storage times in a material trap (878.5$\pm$0.8 s). The experiment described here eliminates loss mechanisms present in previous trap experiments by levitating polarized ultracold neutrons above the surface of an asymmetric storage trap using a repulsive magnetic field gradient so that the stored neutrons do not interact with material trap walls and neutrons in quasi-stable orbits rapidly exit the trap. As a result of this approach and the use of a new in situ neutron detector, the lifetime reported here (877.7 $\pm$ 0.7 (stat) +0.4/-0.2 (sys) s) is the first modern measurement of $\tau_n$ that does not require corrections larger than the quoted uncertainties.Comment: 9 pages, 3 figures, 2 table

Status of the UCNτ experiment

The neutron is the simplest nuclear system that can be used to probe the structure of the weak interaction and search for physics beyond the standard model. Measurements of neutron lifetime and β-decay correlation coefficients with precisions of 0.02% and 0.1%, respectively, would allow for stringent constraints on new physics. The UCNτ experiment uses an asymmetric magneto-gravitational UCN trap with in situ counting of surviving neutrons to measure the neutron lifetime, τ_n = 877.7s (0.7s)_(stat) (+0.4/−0.2s)_(sys). We discuss the recent result from UCNτ, the status of ongoing data collection and analysis, and the path toward a 0.25 s measurement of the neutron lifetime with UCNτ

Seasonal Distribution, Aggregation, and Habitat Selection of Common Carp in Clear Lake, Iowa

The common carp Cyprinus carpio is widely distributed and frequently considered a nuisance species outside its native range. Common carp are abundant in Clear Lake, Iowa, where their presence is both a symptom of degradation and an impediment to improving water quality and the sport fishery. We used radiotelemetry to quantify seasonal distribution, aggregation, and habitat selection of adult and subadult common carp in Clear Lake during 2005–2006 in an effort to guide future control strategies. Over a 22-month period, we recorded 1,951 locations of 54 adults and 60 subadults implanted with radio transmitters. Adults demonstrated a clear tendency to aggregate in an offshore area during the late fall and winter and in shallow, vegetated areas before and during spring spawning. Late-fall and winter aggregations were estimated to include a larger percentage of the tracked adults than spring aggregations. Subadults aggregated in shallow, vegetated areas during the spring and early summer. Our study, when considered in combination with previous research, suggests repeatable patterns of distribution, aggregation, and habitat selection that should facilitate common carp reduction programs in Clear Lake and similar systems

Search for the Neutron Decay n → X + γ, Where X is a Dark Matter Particle

Fornal and Grinstein recently proposed that the discrepancy between two different methods of neutron lifetime measurements, the beam and bottle methods, can be explained by a previously unobserved dark matter decay mode, n → X + γ. We perform a search for this decay mode over the allowed range of energies of the monoenergetic γray for X to be dark matter. A Compton-suppressed high-purity germanium detector is used to identify γrays from neutron decay in a nickel-phosphorous-coated stainless-steel bottle. A combination of Monte Carlo and radioactive source calibrations is used to determine the absolute efficiency for detecting γ rays arising from the dark matter decay mode. We exclude the possibility of a sufficiently strong branch to explain the lifetime discrepancy with 97% confidence

Search for the Neutron Decay \u3cem\u3en\u3c/em\u3e → \u3cem\u3eX\u3c/em\u3e+\u3cem\u3eγ\u3c/em\u3e, Where \u3cem\u3eX\u3c/em\u3e is a Dark Matter Particle

Fornal and Grinstein recently proposed that the discrepancy between two different methods of neutron lifetime measurements, the beam and bottle methods, can be explained by a previously unobserved dark matter decay mode, n → X+γ. We perform a search for this decay mode over the allowed range of energies of the monoenergetic γ ray for X to be dark matter. A Compton-suppressed high-purity germanium detector is used to identify γ rays from neutron decay in a nickel-phosphorous-coated stainless-steel bottle. A combination of Monte Carlo and radioactive source calibrations is used to determine the absolute efficiency for detecting γ rays arising from the dark matter decay mode. We exclude the possibility of a sufficiently strong branch to explain the lifetime discrepancy with 97% confidence