Improved variation calling via an iterative backbone remapping and local assembly method for bacterial genomes

AbstractSequencing data analysis remains limiting and problematic, especially for low complexity repeat sequences and transposon elements due to inherent sequencing errors and short sequence read lengths. We have developed a program, ReviSeq, which uses a hybrid method composed of iterative remapping and local assembly upon a bacterial sequence backbone. Application of this method to six Brucella suis field isolates compared to the newly revised B. suis 1330 reference genome identified on average 13, 15, 19 and 9 more variants per sample than STAMPY/SAMtools, BWA/SAMtools, iCORN and BWA/PINDEL pipelines, and excluded on average 4, 2, 3 and 19 variants per sample, respectively. In total, using this iterative approach, we identified on average 87 variants including SNVs, short INDELs and long INDELs per strain when compared to the reference. Our program outperforms other methods especially for long INDEL calling.The program is available at http://reviseq.sourceforge.net

HEF1, a novel target of Wnt signaling, promotes colonic cell migration and cancer progression

Misregulation of the canonical Wnt/Β-catenin pathway and aberrant activation of Wnt signaling target genes are common in colorectal cancer (CRC) and contribute to cancer progression. Altered expression of human enhancer of filamentation 1 (HEF1; also known as NEDD9 or Cas-L) has been implicated in progression of melanoma, breast, and CRC. However, the regulation of HEF1 and the role of HEF1 in CRC tumorigenesis are not fully understood. We here identify HEF1 as a novel Wnt signaling target. The expression of HEF1 was upregulated by Wnt-3a, Β-catenin, and Dvl2 in a dose-dependent manner, and was suppressed following Β-catenin downregulation by shRNA. In addition, elevated HEF1 mRNA and protein levels were observed in CRC cell lines and primary tumor tissues, as well as in the colon and adenoma polyps of Apc Min/ mice. Moreover, HEF1 levels in human colorectal tumor tissues increased with the tumor grade. Chromatin immunoprecipitation (ChIP) assays and promoter analyses revealed three functional T-cell factor (TCF)-binding sites in the promoter of HEF1 responsible for HEF1 induction by Wnt signaling. Ectopic expression of HEF1 increased cell proliferation and colony formation, while downregulation of HEF1 in SW480 cells by shRNA had the opposite effects and inhibited the xenograft tumor growth. Furthermore, overexpression of HEF1 in SW480 cells promoted cell migration and invasion. Together, our results determined a novel role of HEF1 as a mediator of the canonical Wnt/Β-catenin signaling pathway for cell proliferation, migration, and tumorigenesis, as well as an important player in colorectal tumorigenesis and progression. HEF1 may represent an attractive candidate for drug targeting in CRC. © 2011 Macmillan Publishers Limited All rights reserved

Personalization in Skipforward, an Ontology-Based Distributed Annotation System

Abstract. Skipforward is a distributed annotation system allowing users to enter and browse statements about items and their features. Items can be things such as movies or books; item features are the genre of a movie or the storytelling pace of a book. Whenever multiple users annotate the same item with a statement about the same feature, these individual statements get aggregated by the system. For aggregation, individual user statements are weighted according to a competence metric based on the constrained Pearson correlation, adapted for Skipforward data: A user gets assigned high competence with regard to the feature in question if, for other items and the same feature type, he had a similar opinion to the current user. Since the competence metric is dependent on the user currently viewing the data, the user’s view of the data is completely personalized. In this paper, the personalization aspect as well as the item and expert recommender are presented.

Top network of Vk2 PIC/NIC discriminatory genes generated by Ingenuity Pathway Analysis.

<p>Red/pink color indicates upregulation of the genes (microarray data). Connections of NFkB complex with other genes is shown in blue color.</p

Real-time qPCR validation of changes in expression of eight selected genes observed in microarray analysis.

<p>Bars represent the mean ± SD of fold change relative to growth medium control. At least 3 independent experiments were performed for each treatment. All genes were normalized to GAPDH. Asterisks placed vertically denote p values for each PIC treatment relative to HEC used as a reference. (***p<0.0005, **p<0.005, *p< 0.05; Student t-test)</p

Transcription profile of the 20 discriminatory genes expression in Vk2 cells exposed to candidate microbicides and selected PICs and NICs.

<p>Columns represent treatments, rows represent genes. Gene expression levels are indicated by color: red is for upregulation and green is for downregulation. Expression data are averages from at least six experiments/microarrays for each treatment. Clustering based on 20 PIC/NIC discriminatory genes places C31G (known as causing inflammatory response) to the PIC category, while dextran sulfate (DS) and cellulose sulfate (CS)—into the NIC group.</p

Real-time qPCR validation of changes in expression of eight selected genes observed in the microarray analysis of microbicide candidates.

<p>Experimental details are as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128557#pone.0128557.g005" target="_blank">Fig 5</a>. HEC and TNF-α are added as references.</p

PIC-DG expression following bacterial colonization of Vk2 cells as revealed by quantitative real time RT-PCR.

<p>P. bivia (right) induced strong upregulation of all seven PIC-DEGs, while L. gasseri (left) did not cause any changes. Results are presented as mean ±SD of three experiments.</p