Bivariate genome-wide association study of the growth plasticity of Staphylococcus aureus in coculture with Escherichia coli

SeQual-Stream: approaching stream processing to quality control of NGS datasets

BACKGROUND

Quality control of DNA sequences is an important data preprocessing step in many genomic analyses. However, all existing parallel tools for this purpose are based on a batch processing model, needing to have the complete genetic dataset before processing can even begin. This limitation clearly hinders quality control performance in those scenarios where the dataset must be downloaded from a remote repository and/or copied to a distributed file system for its parallel processing.

RESULTS

In this paper we present SeQual-Stream, a streaming tool that allows performing multiple quality control operations on genomic datasets in a fast, distributed and scalable way. To do so, our approach relies on the Apache Spark framework and the Hadoop Distributed File System (HDFS) to fully exploit the stream paradigm and accelerate the preprocessing of large datasets as they are being downloaded and/or copied to HDFS. The experimental results have shown significant improvements in the execution times of SeQual-Stream when compared to a batch processing tool with similar quality control features, providing a maximum speedup of 2.7[Formula: see text] when processing a dataset with more than 250 million DNA sequences, while also demonstrating good scalability features.

CONCLUSION

Our solution provides a more scalable and higher performance way to carry out quality control of large genomic datasets by taking advantage of stream processing features. The tool is distributed as free open-source software released under the GNU AGPLv3 license and is publicly available to download at https://github.com/UDC-GAC/SeQual-Stream .

Mechanisms of gene regulation by histone degradation in adaptation of yeast: an overview of recent advances

Histones are important component of eukaryotic cells chromatin and consist of arginine and lysine residues. Histones play an important role in the protection of DNA. Their contents significantly affect high-level chromatin structure formation, gene expression, DNA replication, and other important life activities. Protein degradation is an important regulatory mechanism of histone content. Recent studies have revealed that modification of amino acid sequence is directly related to histone breakdown. In addition, histone degradation is closely related to covalent modifications, such as ubiquitination and acetylation, which are considered to be driving factors in gene regulation. Gene regulation is an important mechanism in adaptation to the environment and survival of species. With the introduction of highly efficient technology, various mutations in histones have been identified in yeast. In the field of epigenetics and the transmission of chromatin states, two widely used model organisms are the budding yeast Saccharomyces cerevisiae and Schizosaccharomyces pombe. Higher eukaryotes can use their silent loci to maintain their epigenetic states and providing the base to investigate mechanisms underlying development. Therfore, both species have contributed a plethora of information on these mechanisms in both yeast and higher eukaryotes. This study focuses on the role of histone modifications in controlling telomeric silencing in Saccharomyces cerevisiae and centromeric silencing in S. pombe as examples of genetic loci that demonstrate epigenetic inheritance. In view of recent advances, this review focuses on the post-translational modification of histone amino acid residues and reviews the relationship between histone degradation and amino acid residue modification.

Functional Mapping of Phenotypic Plasticity of Staphylococcus aureus Under Vancomycin Pressure

Phenotypic plasticity is the exhibition of various phenotypic traits produced by a single genotype in response to environmental changes, enabling organisms to adapt to environmental changes by maintaining growth and reproduction. Despite its significance in evolutionary studies, we still know little about the genetic control of phenotypic plasticity. In this study, we designed and conducted a genome-wide association study (GWAS) to reveal genetic architecture of how Staphylococcus aureus strains respond to increasing concentrations of vancomycin (0, 2, 4, and 6 μg/mL) in a time course. We implemented functional mapping, a dynamic model for genetic mapping using longitudinal data, to map specific loci that mediate the growth trajectories of abundance of vancomycin-exposed S. aureus strains. 78 significant single nucleotide polymorphisms were identified following analysis of the whole growth and development process, and seven genes might play a pivotal role in governing phenotypic plasticity to the pressure of vancomycin. These seven genes, SAOUHSC_00020 (walR), SAOUHSC_00176, SAOUHSC_00544 (sdrC), SAOUHSC_02998, SAOUHSC_00025, SAOUHSC_00169, and SAOUHSC_02023, were found to help S. aureus regulate antibiotic pressure. Our dynamic gene mapping technique provides a tool for dissecting the phenotypic plasticity mechanisms of S. aureus under vancomycin pressure, emphasizing the feasibility and potential of functional mapping in the study of bacterial phenotypic plasticity.

Dissecting the Genetic Regulation of Yeast Growth Plasticity in Response to Environmental Changes

Variable individual responses to environmental changes, such as phenotype plasticity, are heritable, with some genotypes being robust and others plastic. This variation for plasticity contributes to variance in complex traits as genotype-by-environment interactions (G × E). However, the genetic basis of this variability in responses to the same external stimuli is still largely unknown. In an earlier study of a large haploid segregant yeast population, genotype-by-genotype-by-environment interactions were found to make important contributions to the release of genetic variation in growth responses to alterations of the growth medium. Here, we explore the genetic basis for heritable variation of different measures of phenotype plasticity in the same dataset. We found that the central loci in the environmentally dependent epistatic networks were associated with overall measures of plasticity, while the specific measures of plasticity identified a more diverse set of loci. Based on this, a rapid one-dimensional genome-wide association (GWA) approach to overall plasticity is proposed as a strategy to efficiently identify key epistatic loci contributing to the phenotype plasticity. The study thus provided both analytical strategies and a deeper understanding of the complex genetic regulation of phenotype plasticity in yeast growth.

Hybrid Polydopamine/Ag Shell-Encapsulated Magnetic Fe3O4 Nanosphere with High Antibacterial Activity

The bacteria, which usually contaminate water environment, often cause terrible infectious diseases thus seriously threaten people's health. To meet the increasing requirement of the public health care, an easily separable nanomaterial with sustainable anti-bacteria performance is required. This work reports a Fe₃O₄@PDA/Ag/PDA core-shell nanosphere in which the Ag nanocrystals immobilized on the magnetic carrier are protected by an external polydopamine (PDA) layer. The magnetic hybrid nanospheres are constructed by a tunable coating method and the particle parameters can be effectively controlled by the experimental condition. The antibacterial potential of the nanospheres is evaluable by using the Staphylococcus aureus and Escherichia coli as the models. The results indicate the Fe₃O₄@PDA/Ag/PDA core-shell nanospheres have a high antibacterial performance by measuring the minimum inhibitory concentration and the minimum bactericidal concentration. Finally, the product is expected to have a sustainable activity because the protecting PDA layer reduce the releasing rate of the Ag⁺ ions and the materials can be magnetically recovered from the media after the disinfection procedure.