Gene expression

Event Date: 
Wednesday, August 27, 2014 - 18:15 - 18:30
Institution: 
UNSW
Title: 

Analysis of gene co-expression networks reveals mechanisms underlying synergistic antifungal treatment in S. cerevisiae

Abstract: 

 
Background: Fungal pathogens are difficult to treat. There are few effective antifungal drugs available, and resistance is emerging. Iron chelators are promising synergents due to the importance of iron availability during host infection, but the mechanistic role of antifungal-chelator combinations is poorly understood. The project analyses cellular pathways that are differentially expressed during the synergistic response to elucidate the mechanisms and targets of drug-chelator treatment.
Method: To measure the effect of synergistic treatment on the S. cerevisiae transcriptome, cells were treated with i) amphotericin B only; ii) a combination of amphotericin B + lactoferrin, an iron chelator; and iii & iv) corresponding matching controls. RNA-seq data were generated using Illumina HiSeq 2000 with biological triplicates multiplexed and randomized across two sequencing lanes. Differential expression analyses were performed using EdgeR, and the results were co-visualized with biological networks using Cytoscape.
Results: Amphotericin B alone resulted in the down-regulation of nine genes involved in ergosterol biosynthesis and the up-regulation of AFT1, a transcription factor involved in iron transport. Amphotericin B + lactoferrin co-treatment halted AFT1 up-regulation and down-regulated genes involved in iron transport. These genes were co-expressed with YAP5, a second transcription factor that co-ordinates the expression of genes that control the nuclear localization of AFT1 and also governs the expression of oxidative stress response genes.

Event Date: 
Wednesday, October 31, 2012 - 07:00 - 08:00
Institution: 
CSIRO
Title: 

Microbial responses to phenanthrene contamination in soil

Abstract: 

 
The effect of phenanthrene on soil microbial community structure and gene expression was evaluated by 16S rRNA gene microbiome analysis and next generation sequencing of community mRNA. Widespread changes in microbial diversity and functional gene content were revealed. Actinobacteria abundances increased markedly with the addition of phenanthrene, in particular that of Arthrobacter and Mycobacterium, and evidence was also obtained for an increase in the abundance of protozoans. The abundance of transcripts annotated as dioxygenases, heavy metal P-type ATPases, thioredoxins and heat shock proteins increased 1.8-7 fold upon phenanthrene amendment, whereas those of general metabolism were little affected. Custom databases constructed with bacterial or fungal PAH metabolism genes were used to further annotate transcripts, and revealed that increases in PAH-degradatory gene expression occurred for all gene groups investigated. Taxonomic determination of mRNA transcripts showed that the actinobacteria were responsible for most of the de novo expression of transcripts associated with dioxygenases, stress response and detoxification genes. This study is the first combining microbiome and metatranscriptomic approaches to describe microbial community responses to a pollutant in soil, offering information on novel in-situ effects which opens up new directions for research in PAH degradation and bioremediation. 

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