Fitness Tradeoffs of Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli

Evolutionary trade-offs occur when selection on one trait has detrimental effects on other traits. In pathogenic microbes, it has been hypothesized that antibiotic resistance trades off with fitness in the absence of antibiotic. Although studies of single resistance mutations support this hypothesis, it is unclear whether trade-offs are maintained over time, due to compensatory evolution and broader effects of genetic background. Here, we leverage natural variation in 39 extraintestinal clinical isolates of Escherichia coli to assess trade-offs between growth rates and resistance to fluoroquinolone and cephalosporin antibiotics. Whole-genome sequencing identifies a broad range of clinically relevant resistance determinants in these strains. We find evidence for a negative correlation between growth rate and antibiotic resistance, consistent with a persistent trade-off bet

Fast and scalable protein motif sequence clustering based on Hadoop framework

In recent years, we are faced with large amounts of sporadic unstructured data on the web. With the explosive growth of such data, there is a growing need for effective methods such as clustering to analyze and extract information. Biological data forms an important part of unstructured data on the web. Protein sequence databases are considered as a primary source of biological data. Clustering can help to organize sequences into homologous and functionally similar groups and can improve the speed of data processing and analysis. Proteins are responsible for most of the activities in cells. The majority of proteins show their function through interaction with other proteins. Hence, prediction of protein interactions is an important research area in the biomedical sciences. Motifs are fragments frequently occurred in protein sequences. A well- known method to specify the protein interaction is based on motif Clustering. Existing works on motif clustering methods share the problem of limitation in the number of clusters. However, regarding the vast amount of motifs and the necessity of a large number of clusters, it seems that an efficient, scalable and fast method is necessary to cluster such large number of sequences. In this paper, we propose a novel approach to cluster a large number of motifs. Our approach includes extracting motifs within protein sequences, feature selection, preprocessing, dimension reduction and utilizing BigFCM (a large-scale fuzzy clustering) on several distributed nodes with Hadoop framework to take the advantage of MapReduce Programming. Experimental Results show very good Performance of our approach

MP-PIPE: A massively parallel protein-protein interaction prediction engine

Interactions among proteins are essential to many biological functions in living cells but experimentally detected interactions represent only a small fraction of the real interaction network. Computational protein interaction prediction methods have become important to augment the experimental methods; in particular sequence based prediction methods that do not require additional data such as homologous sequences or 3D structure information which are often not available. Our Protein Interaction Prediction Engine (PIPE) method falls into this category. Park has recently compared PIPE with the other competing methods and concluded that our method "significantly outperforms the others in terms of recall-precision across both the yeast and human data". Here, we present MP-PIPE, a new massively parallel PIPE implementation for large scale, high throughput protein interaction prediction. MP-PIPE enabled us to perform the first ever complete scan of the entire human protein interaction network; a massively parallel computational experiment which took three months of full time 24/7 computation on a dedicated SUN UltraSparc T2+ based cluster with 50 nodes, 800 processor cores and 6,400 hardware supported threads. The implications for the understanding of human cell function will be significant as biologists are starting to analyze the 130,470 new protein interactions and possible new pathways in Human cells predicted by MP-PIPE

Recent advances in proteinprotein interaction prediction: Experimental and computational methods

Introduction: Proteins within the cell act as part of complex networks, which allow pathways and processes to function. Therefore, understanding how proteins interact is a significant area of current research. Areas covered: This review aims to present an overview of key experimental techniques (yeast two-hybrid, tandem affinity purification and protein microarrays) used to discover proteinprotein interactions (PPIs), as well as to briefly discuss certain computational methods for predicting protein interactions based on gene localization, phylogenetic information, 3D structural modeling or primary protein sequence data. Due to the large-scale applicability of primary sequence-based methods, the authors have chosen to focus on this strategy for our review. There is an emphasis on a recent algorithm called Protein Interaction Prediction Engine (PIPE) that can predict global PPIs. The readers will discover recent advances both in the practical determination of protein interaction and the strategies that are available to attempt to anticipate interactions without the time and costs of experimental work. Expert opinion: Global PPI maps can help understand the biology of complex diseases and facilitate the identification of novel drug target sites. This study describes different techniques used for PPI prediction that we believe will significantly impact the development

Designing anti-Zika virus peptides derived from predicted human-Zika virus protein-protein interactions

The production of anti-Zika virus (ZIKV) therapeutics has become increasingly important as the propagation of the devastating virus continues largely u