TY  - JOUR
A1  - Cui, Pin
A1  - Löber, Ulrike
A1  - Alquezar-Planas, David E.
A1  - Ishida, Yasuko
A1  - Courtiol, Alexandre
A1  - Timms, Peter
A1  - Johnson, Rebecca N.
A1  - Lenz, Dorina
A1  - Helgen, Kristofer M.
A1  - Roca, Alfred L.
A1  - Hartman, Stefanie
A1  - Greenwood, Alex D.
T1  - Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome
JF  - PeerJ
N2  - Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small.
KW  - Integration sites
KW  - Retroviral endogenization
KW  - KoRV
KW  - Target enrichment
KW  - Clustering
Y1  - 2016
U6  - https://doi.org/10.7717/peerj.1847
SN  - 2167-8359
VL  - 4
PB  - PeerJ Inc.
CY  - London
ER  - 
TY  - JOUR
A1  - Vales, Dina
A1  - Dias, Nuno A.
A1  - Rio, Ines
A1  - Matias, Luis
A1  - Silveira, Graca
A1  - Madeira, Jose
A1  - Weber, Michael H.
A1  - Carrilho, Fernando
A1  - Haberland, Christian
T1  - Intraplate seismicity across the Cape Verde swell: A contribution from a temporary seismic network
JF  - Tectonophysics : international journal of geotectonics and the geology and physics of the interior of the earth
N2  - We present an analysis and characterization of the regional seismicity recorded by a temporary broadband seismic network deployed in the Cape Verde archipelago between November 2007 and September 2008.
 The detection of earthquakes was based on spectrograms, allowing the discrimination from low-frequency volcanic signals, resulting in 358 events of which 265 were located, the magnitudes usually being smaller than 3. For the location, a new 1-D P-velocity model was derived for the region showing a crust consistent with an oceanic crustal structure. The seismicity is located mostly offshore the westernmost and geologically youngest areas of the archipelago, near the islands of Santo Antao and Sao Vicente in the NW and Brava and Fogo in the SW. The SW cluster has a lower occurrence rate and corresponds to seismicity concentrated mainly along an alignment between Brava and the Cadamosto seamount presenting normal faulting mechanisms. The existence of the NW cluster, located offshore SW of Santo Antao, was so far unknown and concentrates around a recently recognized submarine cone field; this cluster presents focal depths extending from the crust to the upper mantle and suggests volcanic unrest No evident temporal behaviour could be perceived, although the events tend to occur in bursts of activity lasting a few days. In this recording period, no significant activity was detected at Fogo volcano, the most active volcanic edifice in Cape Verde.
 The seismicity characteristics point mainly to a volcanic origin. The correlation of the recorded seismicity with active volcanic structures agrees with the tendency for a westward migration of volcanic activity in the archipelago as indicated by the geologic record. (C) 2014 Elsevier B.V. All rights reserved.
KW  - Intraplate seismicity
KW  - Clustering
KW  - Local magnitude scale
KW  - Active volcanism
KW  - Cape Verde
KW  - Atlantic Ocean
Y1  - 2014
U6  - https://doi.org/10.1016/j.tecto.2014.09.014
SN  - 0040-1951
SN  - 1879-3266
VL  - 636
SP  - 325
EP  - 337
PB  - Elsevier
CY  - Amsterdam
ER  -