@article{MatosMachadoSchartletal.2015,
  author    = {Matos, I and Machado, M. P. and Schartl, M. and Coelho, M. M.},
  title     = {Gene expression dosage regulation in an allopolyploid fish},
  series = {PLoS ONE},
  volume    = {10},
  journal   = {PLoS ONE},
  number    = {3},
  doi       = {10.1371/journal.pone.0116309},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-143565},
  pages     = {e0116309},
  year      = {2015},
  abstract  = {How allopolyploids are able not only to cope but profit from their condition is a question that remains elusive, but is of great importance within the context of successful allopolyploid evolution. One outstanding example of successful allopolyploidy is the endemic Iberian cyprinid Squalius alburnoides. Previously, based on the evaluation of a few genes, it was reported that the transcription levels between diploid and triploid S. alburnoides were similar. If this phenomenon occurs on a full genomic scale, a wide functional "diploidization'' could be related to the success of these polyploids. We generated RNA-seq data from whole juvenile fish and from adult livers, to perform the first comparative quantitative transcriptomic analysis between diploid and triploid individuals of a vertebrate allopolyploid. Together with an assay to estimate relative expression per cell, it was possible to infer the relative sizes of transcriptomes. This showed that diploid and triploid S. alburnoides hybrids have similar liver transcriptome sizes. This in turn made it valid to directly compare the S. alburnoides RNA-seq transcript data sets and obtain a profile of dosage responses across the S. alburnoides transcriptome. We found that 64\% of transcripts in juveniles' samples and 44\% in liver samples differed less than twofold between diploid and triploid hybrids (similar expression). Yet, respectively 29\% and 15\% of transcripts presented accurate dosage compensation (PAA/PA expression ratio of 1 instead of 1.5). Therefore, an exact functional diploidization of the triploid genome does not occur, but a significant down regulation of gene expression in triploids was observed. However, for those genes with similar expression levels between diploids and triploids, expression is not globally strictly proportional to gene dosage nor is it set to a perfect diploid level. This quantitative expression flexibility may be a strong contributor to overcome the genomic shock, and be an immediate evolutionary advantage of allopolyploids.},
  language  = {en}
}
@article{WestburyTurroGreeneetal.2015,
  author    = {Westbury, Sarah K and Turro, Ernest and Greene, Daniel and Lentaigne, Claire and Kelly, Anne M and Bariana, Tadbir K and Simeoni, Ilenia and Pillois, Xavier and Attwood, Antony and Austin, Steve and Jansen, Sjoert BG and Bakchoul, Tamam and Crisp-Hihn, Abi and Erber, Wendy N and Favier, R{\´e}mi and Foad, Nicola and Gattens, Michael and Jolley, Jennifer D and Liesner, Ri and Meacham, Stuart and Millar, Carolyn M and Nurden, Alan T and Peerlinck, Kathelijne and Perry, David J and Poudel, Pawan and Schulman, Sol and Schulze, Harald and Stephens, Jonathan C and Furie, Bruce and Robinson, Peter N and van Geet, Chris and Rendon, Augusto and Gomez, Keith and Laffan, Michael A and Lambert, Michele P and Nurden, Paquita and Ouwehand, Willem H and Richardson, Sylvia and Mumford, Andrew D and Freson, Kathleen},
  title     = {Human phenotype ontology annotation and cluster analysis to unravel genetic defects in 707 cases with unexplained bleeding and platelet disorders},
  series = {Genome Medicine},
  volume    = {7},
  journal   = {Genome Medicine},
  number    = {36},
  doi       = {10.1186/s13073-015-0151-5},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-143329},
  year      = {2015},
  abstract  = {Background: Heritable bleeding and platelet disorders (BPD) are heterogeneous and frequently have an unknown genetic basis. The BRIDGE-BPD study aims to discover new causal genes for BPD by high throughput sequencing using cluster analyses based on improved and standardised deep, multi-system phenotyping of cases. Methods: We report a new approach in which the clinical and laboratory characteristics of BPD cases are annotated with adapted Human Phenotype Ontology (HPO) terms. Cluster analyses are then used to characterise groups of cases with similar HPO terms and variants in the same genes. Results: We show that 60\% of index cases with heritable BPD enrolled at 10 European or US centres were annotated with HPO terms indicating abnormalities in organ systems other than blood or blood-forming tissues, particularly the nervous system. Cases within pedigrees clustered closely together on the bases of their HPO-coded phenotypes, as did cases sharing several clinically suspected syndromic disorders. Cases subsequently found to harbour variants in ACTN1 also clustered closely, even though diagnosis of this recently described disorder was not possible using only the clinical and laboratory data available to the enrolling clinician. Conclusions: These findings validate our novel HPO-based phenotype clustering methodology for known BPD, thus providing a new discovery tool for BPD of unknown genetic basis. This approach will also be relevant for other rare diseases with significant genetic heterogeneity.},
  language  = {en}
}
@article{MurakawaHinzMothesetal.2015,
  author    = {Murakawa, Yasuhiro and Hinz, Michael and Mothes, Janina and Schuetz, Anja and Uhl, Michael and Wyler, Emanuel and Yasuda, Tomoharu and Mastrobuoni, Guido and Friedel, Caroline C. and D{\"o}lken, Lars and Kempa, Stefan and Schmidt-Supprian, Marc and Bl{\"u}thgen, Nils and Backofen, Rolf and Heinemann, Udo and Wolf, Jana and Scheidereit, Claus and Landthaler, Markus},
  title     = {RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-\(\kappa\)B pathway},
  series = {Nature Communications},
  volume    = {6},
  journal   = {Nature Communications},
  number    = {7367},
  doi       = {10.1038/ncomms8367},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-151596},
  year      = {2015},
  abstract  = {The RNA-binding protein RC3H1 (also known as ROQUIN) promotes TNF\(\alpha\) mRNA decay via a 3'UTR constitutive decay element (CDE). Here we applied PAR-CLIP to human RC3H1 to identify ~3,800 mRNA targets with >16,000 binding sites. A large number of sites are distinct from the consensus CDE and revealed a structure-sequence motif with U-rich sequences embedded in hairpins. RC3H1 binds preferentially short-lived and DNA damage-induced mRNAs, indicating a role of this RNA-binding protein in the post-transcriptional regulation of the DNA damage response. Intriguingly, RC3H1 affects expression of the NF-\(\kappa\)B pathway regulators such as I\(\kappa\)B\(\alpha\) and A20. RC3H1 uses ROQ and Zn-finger domains to contact a binding site in the A20 3'UTR, demonstrating a not yet recognized mode of RC3H1 binding. Knockdown of RC3H1 resulted in increased A20 protein expression, thereby interfering with I\(\kappa\)B kinase and NF-\(\kappa\)B activities, demonstrating that RC3H1 can modulate the activity of the IKK/NF-\(\kappa\)B pathway.},
  language  = {en}
}
@article{SherifInceManiucetal.2015,
  author    = {Sherif, Mohammad A. and Ince, H{\"u}seyin and Maniuc, Octavian and Reiter, Therese and Voelker, Wolfram and Ertl, Georg and {\"O}ner, Alper},
  title     = {Two-dimensional transesophageal echocardiography for aortic annular sizing in patients undergoing transcatheter aortic valve implantation},
  series = {BMC Cardiovascular Disorders},
  volume    = {15},
  journal   = {BMC Cardiovascular Disorders},
  number    = {181},
  doi       = {10.1186/s12872-015-0181-3},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-136002},
  year      = {2015},
  abstract  = {Background: Accurate preoperative assessment of the aortic annulus dimension is crucial for successful transcatheter aortic valve implantation (TAVI). In this study we examined the accuracy of a novel method using two-dimensional transesophageal echocardiography (2D-TEE) for measurement of the aortic annulus. Methods: We evaluated the theoretical impact of the measurement of the annulus diameter and area using the circumcircle of a triangle method on the decision to perform the procedure and choice of the prosthesis size. Results: Sixty-three consecutive patients were scheduled for TAVI. Mean age was 82 +/- 4 years, and 25 patients (55.6 \%) were female. Mean aortic annulus diameter was 20.3 +/- 2.2 mm assessed by TEE on the mid-esophageal long-axis view and 23.9 +/- 2.3 mm using CT (p < 0.001). There was a tendency for the TEE derived areas using the new method to be higher (p < 0.001). The TEE measurements were on average 42.33 mm(2) higher than the CT measurements without an evidence of a systematic over-or under-sizing (p = 1.00). Agreement between TEE and CT chosen valve sizes was good overall (kappa = 0.67 and weighted kappa = 0.71). For patients who turned out to have no AR, the two methods agreed in 84.6 \% of patients. Conclusions: CT remanis the gold standard in sizing of the aortic valve annulus. Nevertheless, sizing of the aortic valve annulus using TEE derived area may be helpful. The impact of integration of this method in the algorithm of aortic annulus sizing on the outcome of patients undergoing TAVI should be examined in future studies.},
  language  = {en}
}