162 research outputs found
Geographic variation in the calling songs and genetics of Bartram's round-winged katydid Amblycorypha bartrami (Tettigoniidae, Phaneropterinae) reveal new species
Previous work on Bartram's round-winged katydid, Amblycorypha bartrami Walker, found inconsistencies in song variation across the species' range. Individuals of purported populations of A. bartrami from sandhills across the southeastern US were collected, recorded, and their genes were sequenced to better understand their population structure and evolution. Significant differences in songs, morphology, and genetics were found among populations from Alabama (AL), Georgia (GA), North Carolina (NC), and South Carolina (SC), and they differed from those of individuals collected from the type locality in Florida (FL). Males from all populations produced songs composed of a series of similar syllables, but they differed in the rates at which syllables were produced as a function of temperature. At temperatures of 25°C, the calling songs of males from populations in northern AL and GA were found to have the highest syllable rates, those from SC had the lowest rates, and those from NC were found to produce songs with doublet syllables at rates that were intermediate between those of males from FL and those of AL and GA. These song differences formed the basis for cluster analyses and principal component analyses, which showed significant clustering and differences in song spectra and morphology among the song morphs. A Bayesian multi-locus, multi-species coalescent analysis found significant divergences from a panmictic population for the song morphs. Populations from GA and AL are closely related to those of A. bartrami in FL, whereas populations from NC and SC are closely related to each other and differ from the other three. Large river systems may have been important in isolating these populations of flightless katydids. Based on the results of our analyses of songs, morphology, and genetics, three new species of round-winged katydids from the southeastern coastal plain and piedmont are described
Observation of low-lying isomeric states in Cs: a new avenue for dark matter and solar neutrino detection in xenon detectors
We report on new measurements establishing the existence of low-lying
isomeric states in Cs using rays produced in
Xe(p,n)Cs reactions. Two states with ~ns
lifetimes are placed in the decay sequence of the Cs levels that are
populated in charged-current interactions of solar neutrinos and fermionic dark
matter with Xe. Xenon-based experiments can therefore exploit a
delayed-coincidence tag of these interactions, greatly suppressing backgrounds
to enable spectroscopic studies of solar neutrinos and dark matter.Comment: Supplemental material available upon request. Version accepted by
Phys.Rev.Let
Pseudo–Messenger RNA: Phantoms of the Transcriptome
The mammalian transcriptome harbours shadowy entities that resist classification and analysis. In analogy with pseudogenes, we define pseudo–messenger RNA to be RNA molecules that resemble protein-coding mRNA, but cannot encode full-length proteins owing to disruptions of the reading frame. Using a rigorous computational pipeline, which rules out sequencing errors, we identify 10,679 pseudo–messenger RNAs (approximately half of which are transposon-associated) among the 102,801 FANTOM3 mouse cDNAs: just over 10% of the FANTOM3 transcriptome. These comprise not only transcribed pseudogenes, but also disrupted splice variants of otherwise protein-coding genes. Some may encode truncated proteins, only a minority of which appear subject to nonsense-mediated decay. The presence of an excess of transcripts whose only disruptions are opal stop codons suggests that there are more selenoproteins than currently estimated. We also describe compensatory frameshifts, where a segment of the gene has changed frame but remains translatable. In summary, we survey a large class of non-standard but potentially functional transcripts that are likely to encode genetic information and effect biological processes in novel ways. Many of these transcripts do not correspond cleanly to any identifiable object in the genome, implying fundamental limits to the goal of annotating all functional elements at the genome sequence level
Discovery and Rossiter-McLaughlin Effect of Exoplanet Kepler-8b
We report the discovery and the Rossiter-McLaughlin effect of Kepler-8b, a
transiting planet identified by the NASA Kepler Mission. Kepler photometry and
Keck-HIRES radial velocities yield the radius and mass of the planet around
this F8IV subgiant host star. The planet has a radius RP = 1.419 RJ and a mass,
MP = 0.60 MJ, yielding a density of 0.26 g cm^-3, among the lowest density
planets known. The orbital period is P = 3.523 days and orbital semima jor axis
is 0.0483+0.0006/-0.0012 AU. The star has a large rotational v sin i of 10.5
+/- 0.7 km s^-1 and is relatively faint (V = 13.89 mag), both properties
deleterious to precise Doppler measurements. The velocities are indeed noisy,
with scatter of 30 m s^-1, but exhibit a period and phase consistent with the
planet implied by the photometry. We securely detect the Rossiter-McLaughlin
effect, confirming the planet's existence and establishing its orbit as
prograde. We measure an inclination between the projected planetary orbital
axis and the projected stellar rotation axis of lambda = -26.9 +/- 4.6 deg,
indicating a moderate inclination of the planetary orbit. Rossiter-McLaughlin
measurements of a large sample of transiting planets from Kepler will provide a
statistically robust measure of the true distribution of spin-orbit
orientations for hot jupiters in general.Comment: 26 pages, 8 figures, 2 tables; In preparation for submission to the
Astrophysical Journa
Planetary Candidates Observed by Kepler. VIII. A Fully Automated Catalog With Measured Completeness and Reliability Based on Data Release 25
We present the Kepler Object of Interest (KOI) catalog of transiting
exoplanets based on searching four years of Kepler time series photometry (Data
Release 25, Q1-Q17). The catalog contains 8054 KOIs of which 4034 are planet
candidates with periods between 0.25 and 632 days. Of these candidates, 219 are
new and include two in multi-planet systems (KOI-82.06 and KOI-2926.05), and
ten high-reliability, terrestrial-size, habitable zone candidates. This catalog
was created using a tool called the Robovetter which automatically vets the
DR25 Threshold Crossing Events (TCEs, Twicken et al. 2016). The Robovetter also
vetted simulated data sets and measured how well it was able to separate TCEs
caused by noise from those caused by low signal-to-noise transits. We discusses
the Robovetter and the metrics it uses to sort TCEs. For orbital periods less
than 100 days the Robovetter completeness (the fraction of simulated transits
that are determined to be planet candidates) across all observed stars is
greater than 85%. For the same period range, the catalog reliability (the
fraction of candidates that are not due to instrumental or stellar noise) is
greater than 98%. However, for low signal-to-noise candidates between 200 and
500 days around FGK dwarf stars, the Robovetter is 76.7% complete and the
catalog is 50.5% reliable. The KOI catalog, the transit fits and all of the
simulated data used to characterize this catalog are available at the NASA
Exoplanet Archive.Comment: 61 pages, 23 Figures, 9 Tables, Accepted to The Astrophysical Journal
Supplement Serie
Planet Occurrence within 0.25 AU of Solar-type Stars from Kepler
We report the distribution of planets as a function of planet radius (R_p),
orbital period (P), and stellar effective temperature (Teff) for P < 50 day
orbits around GK stars. These results are based on the 1,235 planets (formally
"planet candidates") from the Kepler mission that include a nearly complete set
of detected planets as small as 2 Earth radii (Re). For each of the 156,000
target stars we assess the detectability of planets as a function of R_p and P.
We also correct for the geometric probability of transit, R*/a. We consider
first stars within the "solar subset" having Teff = 4100-6100 K, logg =
4.0-4.9, and Kepler magnitude Kp < 15 mag. We include only those stars having
noise low enough to permit detection of planets down to 2 Re. We count planets
in small domains of R_p and P and divide by the included target stars to
calculate planet occurrence in each domain. Occurrence of planets varies by
more than three orders of magnitude and increases substantially down to the
smallest radius (2 Re) and out to the longest orbital period (50 days, ~0.25
AU) in our study. For P < 50 days, the radius distribution is given by a power
law, df/dlogR= k R^\alpha. This rapid increase in planet occurrence with
decreasing planet size agrees with core-accretion, but disagrees with
population synthesis models. We fit occurrence as a function of P to a power
law model with an exponential cutoff below a critical period P_0. For smaller
planets, P_0 has larger values, suggesting that the "parking distance" for
migrating planets moves outward with decreasing planet size. We also measured
planet occurrence over Teff = 3600-7100 K, spanning M0 to F2 dwarfs. The
occurrence of 2-4 Re planets in the Kepler field increases with decreasing
Teff, making these small planets seven times more abundant around cool stars
than the hottest stars in our sample. [abridged]Comment: Submitted to ApJ, 22 pages, 10 figure
Planetary Candidates Observed by Kepler, III: Analysis of the First 16 Months of Data
New transiting planet candidates are identified in sixteen months (May 2009 -
September 2010) of data from the Kepler spacecraft. Nearly five thousand
periodic transit-like signals are vetted against astrophysical and instrumental
false positives yielding 1,091 viable new planet candidates, bringing the total
count up to over 2,300. Improved vetting metrics are employed, contributing to
higher catalog reliability. Most notable is the noise-weighted robust averaging
of multi-quarter photo-center offsets derived from difference image analysis
which identifies likely background eclipsing binaries. Twenty-two months of
photometry are used for the purpose of characterizing each of the new
candidates. Ephemerides (transit epoch, T_0, and orbital period, P) are
tabulated as well as the products of light curve modeling: reduced radius
(Rp/R*), reduced semi-major axis (d/R*), and impact parameter (b). The largest
fractional increases are seen for the smallest planet candidates (197% for
candidates smaller than 2Re compared to 52% for candidates larger than 2Re) and
those at longer orbital periods (123% for candidates outside of 50-day orbits
versus 85% for candidates inside of 50-day orbits). The gains are larger than
expected from increasing the observing window from thirteen months (Quarter 1--
Quarter 5) to sixteen months (Quarter 1 -- Quarter 6). This demonstrates the
benefit of continued development of pipeline analysis software. The fraction of
all host stars with multiple candidates has grown from 17% to 20%, and the
paucity of short-period giant planets in multiple systems is still evident. The
progression toward smaller planets at longer orbital periods with each new
catalog release suggests that Earth-size planets in the Habitable Zone are
forthcoming if, indeed, such planets are abundant.Comment: Submitted to ApJS. Machine-readable tables are available at
http://kepler.nasa.gov, http://archive.stsci.edu/kepler/results.html, and the
NASA Exoplanet Archiv
Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.
BACKGROUND: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS: The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS: Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution
Tryptophan degradation in irritable bowel syndrome: evidence of indoleamine 2,3-dioxygenase activation in a male cohort
<p>Abstract</p> <p>Background</p> <p>Irritable bowel syndrome (IBS) is a common disorder that affects 10–15% of the population. Although characterised by a lack of reliable biological markers, the disease state is increasingly viewed as a disorder of the brain-gut axis. In particular, accumulating evidence points to the involvement of both the central and peripheral serotonergic systems in disease symptomatology. Furthermore, altered tryptophan metabolism and indoleamine 2,3-dioxygenase (IDO) activity are hallmarks of many stress-related disorders. The kynurenine pathway of tryptophan degradation may serve to link these findings to the low level immune activation recently described in IBS. In this study, we investigated tryptophan degradation in a male IBS cohort (n = 10) and control subjects (n = 26).</p> <p>Methods</p> <p>Plasma samples were obtained from patients and healthy controls. Tryptophan and its metabolites were measured by high performance liquid chromatography (HPLC) and neopterin, a sensitive marker of immune activation, was measured using a commercially available ELISA assay.</p> <p>Results</p> <p>Both kynurenine levels and the kynurenine:tryptophan ratio were significantly increased in the IBS cohort compared with healthy controls. Neopterin was also increased in the IBS subjects and the concentration of the neuroprotective metabolite kynurenic acid was decreased, as was the kynurenic acid:kynurenine ratio.</p> <p>Conclusion</p> <p>These findings suggest that the activity of IDO, the immunoresponsive enzyme which is responsible for the degradation of tryptophan along this pathway, is enhanced in IBS patients relative to controls. This study provides novel evidence for an immune-mediated degradation of tryptophan in a male IBS population and identifies the kynurenine pathway as a potential source of biomarkers in this debilitating condition.</p
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched cDNAs. The previous dataset, FANTOM2, comprised 60,770 full-length enriched cDNAs. Functional annotation revealed that this cDNA dataset contained only about half of the estimated number of mouse protein-coding genes, indicating that a number of cDNAs still remained to be collected and identified. To pursue the complete gene catalog that covers all predicted mouse genes, cloning and sequencing of full-length enriched cDNAs has been continued since FANTOM2. In FANTOM3, 42,031 newly isolated cDNAs were subjected to functional annotation, and the annotation of 4,347 FANTOM2 cDNAs was updated. To accomplish accurate functional annotation, we improved our automated annotation pipeline by introducing new coding sequence prediction programs and developed a Web-based annotation interface for simplifying the annotation procedures to reduce manual annotation errors. Automated coding sequence and function prediction was followed with manual curation and review by expert curators. A total of 102,801 full-length enriched mouse cDNAs were annotated. Out of 102,801 transcripts, 56,722 were functionally annotated as protein coding (including partial or truncated transcripts), providing to our knowledge the greatest current coverage of the mouse proteome by full-length cDNAs. The total number of distinct non-protein-coding transcripts increased to 34,030. The FANTOM3 annotation system, consisting of automated computational prediction, manual curation, and final expert curation, facilitated the comprehensive characterization of the mouse transcriptome, and could be applied to the transcriptomes of other species
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