scholarly journals Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

2016 ◽  
Author(s):  
John A. Lees ◽  
Minna Vehkala ◽  
Niko Välimäki ◽  
Simon R. Harris ◽  
Claire Chewapreecha ◽  
...  
Keyword(s):  
Enrichment Analysis ◽  
Genetic Associations ◽  
Human Pathogens ◽  
Bacterial Genomes ◽  
Sequence Element ◽  
Clonal Population ◽  
Sequence Elements ◽  
String Mining ◽  
Clonal Population Structure ◽  
Element Enrichment

AbstractBacterial genomes vary extensively in terms of both gene content and gene sequence – this plasticity hampers the use of traditional SNP-based methods for identifying all genetic associations with phenotypic variation. Here we introduce a computationally scalable and widely applicable statistical method (SEER) for the identification of sequence elements that are significantly enriched in a phenotype of interest. SEER is applicable to even tens of thousands of genomes by counting variable-length k-mers using a distributed string-mining algorithm. Robust options are provided for association analysis that also correct for the clonal population structure of bacteria. Using large collections of genomes of the major human pathogensStreptococcus pneumoniaeandStreptococcus pyogenes, SEER identifies relevant previously characterised resistance determinants for several antibiotics and discovers potential novel factors related to the invasiveness ofS. pyogenes. We thus demonstrate that our method can answer important biologically and medically relevant questions.

scholarly journals Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
John A. Lees ◽  
Minna Vehkala ◽  
Niko Välimäki ◽  
Simon R. Harris ◽  
Claire Chewapreecha ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Enrichment Analysis ◽  
Sequence Element ◽  
Element Enrichment

scholarly journals "Clonal" population structure of the malaria agent Plasmodium falciparum in high-infection regions

2005 ◽  
Vol 102 (48) ◽  
pp. 17388-17393 ◽  
Author(s):  
F. G. Razakandrainibe ◽  
P. Durand ◽  
J. C. Koella ◽  
T. De Meeus ◽  
F. Rousset ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Population Structure ◽  
Clonal Population ◽  
High Infection ◽  
Clonal Population Structure

An AP1-binding site in the c-fos gene can mediate induction by epidermal growth factor and 12-O-tetradecanoyl phorbol-13-acetate

1989 ◽  
Vol 9 (3) ◽  
pp. 1327-1331
Author(s):  
T M Fisch ◽  
R Prywes ◽  
R G Roeder
Keyword(s):  
Growth Factor ◽  
Epidermal Growth Factor ◽  
Binding Site ◽  
Tumor Promoter ◽  
Consensus Binding Site ◽  
Sequence Element ◽  
Fos Protein ◽  
Sequence Elements ◽  
Epidermal Growth ◽  
Serum Response

We have demonstrated that two sequence elements in the c-fos promoter can mediate the response of the gene to epidermal growth factor and the tumor promoter 12-O-tetradecanoyl phorbol-13-acetate (TPA). The first is the previously described serum response element. The second is a sequence element highly homologous to the consensus binding site for the HeLa cell transcription factor AP1. Although recent reports have shown that fos protein binds to AP1-binding sites through an interaction with AP1 protein and have raised the speculation that fos protein may negatively regulate expression of the c-fos gene via this interaction, we found no role for the AP1 consensus homology in the downregulation of c-fos expression following induction by epidermal growth factor and TPA.

scholarly journals Dynamics of Genome Architecture in Rhizobium sp. Strain NGR234

2002 ◽  
Vol 184 (1) ◽  
pp. 171-176 ◽  
Author(s):  
Patrick Mavingui ◽  
Margarita Flores ◽  
Xianwu Guo ◽  
Guillermo Dávila ◽  
Xavier Perret ◽  
...  
Keyword(s):  
Large Scale ◽  
Insertion Sequence ◽  
Biological Significance ◽  
Genome Architecture ◽  
Bacterial Genomes ◽  
Symbiotic Plasmid ◽  
Sequence Elements ◽  
Dynamic Structures ◽  
Genome Analyses ◽  
Insertion Sequence Elements

ABSTRACT Bacterial genomes are usually partitioned in several replicons, which are dynamic structures prone to mutation and genomic rearrangements, thus contributing to genome evolution. Nevertheless, much remains to be learned about the origins and dynamics of the formation of bacterial alternative genomic states and their possible biological consequences. To address these issues, we have studied the dynamics of the genome architecture in Rhizobium sp. strain NGR234 and analyzed its biological significance. NGR234 genome consists of three replicons: the symbiotic plasmid pNGR234a (536,165 bp), the megaplasmid pNGR234b (>2,000 kb), and the chromosome (>3,700 kb). Here we report that genome analyses of cell siblings showed the occurrence of large-scale DNA rearrangements consisting of cointegrations and excisions between the three replicons. As a result, four new genomic architectures have emerged. Three consisted of the cointegrates between two replicons: chromosome-pNGR234a, chromosome-pNGR234b, and pNGR234a-pNGR234b. The other consisted of a cointegrate of the three replicons (chromosome-pNGR234a-pNGR234b). Cointegration and excision of pNGR234a with either the chromosome or pNGR234b were studied and found to proceed via a Campbell-type mechanism, mediated by insertion sequence elements. We provide evidence showing that changes in the genome architecture did not alter the growth and symbiotic proficiency of Rhizobium derivatives.

scholarly journals PyClone: statistical inference of clonal population structure in cancer

2014 ◽  
Vol 11 (4) ◽  
pp. 396-398 ◽  
Author(s):  
Andrew Roth ◽  
Jaswinder Khattra ◽  
Damian Yap ◽  
Adrian Wan ◽  
Emma Laks ◽  
...  
Keyword(s):  
Population Structure ◽  
Statistical Inference ◽  
Clonal Population ◽  
Clonal Population Structure

scholarly journals Clonal population structure of encapsulated Haemophilus influenzae.

1988 ◽  
Vol 56 (8) ◽  
pp. 1837-1845 ◽  
Author(s):  
J M Musser ◽  
J S Kroll ◽  
E R Moxon ◽  
R K Selander
Keyword(s):  
Population Structure ◽  
Haemophilus Influenzae ◽  
Clonal Population ◽  
Clonal Population Structure

scholarly journals The resistome of common human pathogens

2017 ◽  
Author(s):  
Christian Munck ◽  
Mostafa M. Hashim Ellabaan ◽  
Michael Schantz Klausen ◽  
Morten O.A. Sommer
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Pathogens ◽  
Antibiotic Resistance Genes ◽  
Gene Clusters ◽  
Species Level ◽  
Natural Environments ◽  
Human Pathogens ◽  
Bacterial Genomes ◽  
Risk Ranking

AbstractGenes capable of conferring resistance to clinically used antibiotics have been found in many different natural environments. However, a concise overview of the resistance genes found in common human bacterial pathogens is lacking, which complicates risk ranking of environmental reservoirs. Here, we present an analysis of potential antibiotic resistance genes in the 17 most common bacterial pathogens isolated from humans. We analyzed more than 20,000 bacterial genomes and defined a clinical resistome as the set of resistance genes found across these genomes. Using this database, we uncovered the co-occurrence frequencies of the resistance gene clusters within each species enabling identification of co-dissemination and co-selection patterns. The resistance genes identified in this study represent the subset of the environmental resistome that is clinically relevant and the dataset and approach provides a baseline for further investigations into the abundance of clinically relevant resistance genes across different environments. To facilitate an easy overview the data is presented at the species level at www.resistome.biosustain.dtu.dk.

Different sequence elements are required for function of the cauliflower mosaic virus polyadenylation site in Saccharomyces cerevisiae compared with in plants

1992 ◽  
Vol 12 (5) ◽  
pp. 2322-2330
Author(s):  
S Irniger ◽  
H Sanfaçon ◽  
C M Egli ◽  
G H Braus
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mosaic Virus ◽  
Cauliflower Mosaic Virus ◽  
Yeast Cells ◽  
Polyadenylation Site ◽  
Proper Function ◽  
Single Point Mutation ◽  
Dependent Manner ◽  
Sequence Element ◽  
Sequence Elements

We show that the polyadenylation site derived from the plant cauliflower mosaic virus (CaMV) is specifically functional in the yeast Saccharomyces cerevisiae. The mRNA 3' endpoints were mapped at the same position in yeast cells as in plants, and the CaMV polyadenylation site was recognized in an orientation-dependent manner. Mutational analysis of the CaMV 3'-end-formation signal revealed that multiple elements are essential for proper activity in yeast cells, including two upstream elements that are situated more than 100 and 43 to 51 nucleotides upstream of the poly(A) addition site and the sequences at or near the poly(A) addition site. A comparison of the sequence elements that are essential for proper function of the CaMV signal in yeast cells and plants showed that both organisms require a distal and a proximal upstream element but that these sequence elements are not identical in yeast cells and plants. The key element for functioning of the CaMV signal in yeast cells is the sequence TAGTATGTA, which is similar to a sequence previously proposed to act in yeast cells as a bipartite signal, namely, TAG ... TATGTA. Deletion of this sequence in the CaMV polyadenylation signal abolished 3'-end formation in yeast cells, and a single point mutation in this motif reduced the activity of the CaMV signal to below 15%. These results indicate that the bipartite sequence element acts as a signal for 3'-end formation in yeast cells but only together with other cis-acting elements.

scholarly journals Regional imaging genetic enrichment analysis

2019 ◽  
Vol 36 (8) ◽  
pp. 2554-2560
Author(s):  
Xiaohui Yao ◽  
Shan Cong ◽  
Jingwen Yan ◽  
Shannon L Risacher ◽  
Andrew J Saykin ◽  
...  
Keyword(s):  
Statistical Power ◽  
Enrichment Analysis ◽  
Genetic Effects ◽  
Imaging Genetics ◽  
Supplementary Information ◽  
Nucleotide Polymorphisms ◽  
Genetic Associations ◽  
Specific Expression ◽  
Positron Emission ◽  
Annotation Information

Abstract Motivation Brain imaging genetics aims to reveal genetic effects on brain phenotypes, where most studies examine phenotypes defined on anatomical or functional regions of interest (ROIs) given their biologically meaningful interpretation and modest dimensionality compared with voxelwise approaches. Typical ROI-level measures used in these studies are summary statistics from voxelwise measures in the region, without making full use of individual voxel signals. Results In this article, we propose a flexible and powerful framework for mining regional imaging genetic associations via voxelwise enrichment analysis, which embraces the collective effect of weak voxel-level signals and integrates brain anatomical annotation information. Our proposed method achieves three goals at the same time: (i) increase the statistical power by substantially reducing the burden of multiple comparison correction; (ii) employ brain annotation information to enable biologically meaningful interpretation and (iii) make full use of fine-grained voxelwise signals. We demonstrate our method on an imaging genetic analysis using data from the Alzheimer’s Disease Neuroimaging Initiative, where we assess the collective regional genetic effects of voxelwise FDG-positron emission tomography measures between 116 ROIs and 565 373 single-nucleotide polymorphisms. Compared with traditional ROI-wise and voxelwise approaches, our method identified 2946 novel imaging genetic associations in addition to 33 ones overlapping with the two benchmark methods. In particular, two newly reported variants were further supported by transcriptome evidences from region-specific expression analysis. This demonstrates the promise of the proposed method as a flexible and powerful framework for exploring imaging genetic effects on the brain. Availability and implementation The R code and sample data are freely available at https://github.com/lshen/RIGEA. Supplementary information Supplementary data are available at Bioinformatics online.

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