RNAsik: A Pipeline for complete and reproducible RNA-seq analysis that runs anywhere with speed and ease

Tsyganov, Kirill; Perry, Andrew; Archer, Stuart K.; Powell, David R.

doi:10.21105/joss.00583

Cited by 45 publications

(32 citation statements)

References 11 publications

(11 reference statements)

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“…Sequencing reads were processed using an in house pipeline consisting of sabre tools (https://github.com/ serine/sabre) and RNAsik [20]. Samples were demultiplexed with a fork of sabre tools with the commands below.…”

Section: Demultiplexing and Mappingmentioning

confidence: 99%

Urban air particulate matter induces mitochondrial dysfunction in human olfactory mucosal cells

et al. 2020

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Background: The adverse effects of air pollutants including particulate matter (PM) on the central nervous system is increasingly reported by epidemiological, animal and post-mortem studies in the last decade. Oxidative stress and inflammation are key consequences of exposure to PM although little is known of the exact mechanism. The association of PM exposure with deteriorating brain health is speculated to be driven by PM entry via the olfactory system. How air pollutants affect this key entry site remains elusive. In this study, we investigated effects of urban size-segregated PM on a novel cellular model: primary human olfactory mucosal (hOM) cells. Results: Metabolic activity was reduced following 24-h exposure to PM without evident signs of toxicity. Results from cytometric bead array suggested a mild inflammatory response to PM exposure. We observed increased oxidative stress and caspase-3/7 activity as well as perturbed mitochondrial membrane potential in PM-exposed cells. Mitochondrial dysfunction was further verified by a decrease in mitochondria-dependent respiration. Transient suppression of the mitochondria-targeted gene, neuronal pentraxin 1 (NPTX1), was carried out, after being identified to be up-regulated in PM 2.5-1 treated cells via RNA sequencing. Suppression of NPTX1 in cells exposed to PM did not restore mitochondrial defects resulting from PM exposure. In contrast, PM-induced adverse effects were magnified in the absence of NPTX1, indicating a critical role of this protein in protection against PM effects in hOM cells. Conclusion: Key mitochondrial functions were perturbed by urban PM exposure in a physiologically relevant cellular model via a mechanism involving NPTX1. In addition, inflammatory response and early signs of apoptosis accompanied mitochondrial dysfunction during exposure to PM. Findings from this study contribute to increased understanding of harmful PM effects on human health and may provide information to support mitigation strategies targeted at air pollution.

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Section: Demultiplexing and Mappingmentioning

confidence: 99%

Urban air particulate matter induces mitochondrial dysfunction in human olfactory mucosal cells

et al. 2020

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“…Reads were assembled using Spades v3.12.0 (67) with a coverage cutoff of 10 in ‘careful’ mode. To identify variants, the filtered sequencing data was mapped back onto the assemblies using BWA (68) as implemented in RNAsik v1.5.0 (69). Both phage-sensitive (S) and phage-resistant (R) sequencing data was mapped back onto each of the genome assemblies from S and R isolates, resulting in 4 alignment files per strain pair (S on S; S on R; R on S; and R on R).…”

Section: Methodsmentioning

confidence: 99%

Bacteriophages targeting Acinetobacter baumannii capsule induce antimicrobial resensitization

Altamirano

Forsyth

Patwa

et al. 2020

Preprint

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21Carbapenem-resistant Acinetobacter baumannii is responsible for frequent, hard-to-treat and often fatal 22 healthcare-associated infections. Phage therapy, the use of viruses that infect and kill bacteria, is an approach 23 gaining significant clinical interest to combat antibiotic-resistant infections. However, a major limitation is that 24 bacteria can develop resistance against phages. Here, we isolated phages with activity against a panel of A.25 baumannii strains and focused on clinical isolates AB900 and A9844 and their phages for detailed 26 characterization. As expected, coincubation of the phages with their hosts in vitro resulted in the emergence of 27 phage-resistant bacterial mutants. Genome sequence analysis revealed that phage-resistant mutants harbored 28 loss-of-function mutations in genes from the K locus, responsible for the biosynthesis of the bacterial capsule. 29Using molecular biology techniques, phage adsorption assays, and quantitative evaluation of capsule 30 production, we established that the bacterial capsule serves as the primary receptor for these phages. As a 31 collateral phenotype of impaired capsule production, the phage-resistant strains could not form biofilms, became 32 fully sensitized to the human complement system, showed increased susceptibility to beta-lactam antibiotics, 33 and became vulnerable to additional phages. Finally, in a murine model of bacteremia, the phage-resistant A. 34 baumannii demonstrated a diminished capacity to colonize blood and solid tissues. This study demonstrates 35 that phages can be used not only for their lytic activity but, if combined with a posteriori knowledge of their 36 receptors and the mechanism of bacterial resistance, for their potential synergy with other antimicrobial agents, 37 thus providing even broader clinical options for phage therapy. 39 Keywords 40Phage therapy, Acinetobacter baumannii, bacterial capsule, phage receptors, antimicrobial resistance. 41 42 2 Introduction 43In 2019, antimicrobial resistance was listed by the World Health Organization (WHO) as one of the top 44 ten threats to global health (1). Multidrug resistant (MDR) infections are consistently associated with poor clinical 45 outcomes and represent a significant financial burden on the healthcare system (2, 3). Also in 2019, the WHO 46 and Centers for Disease Control and Prevention (CDC) prioritized carbapenem-resistant Acinetobacter 47 baumannii as a pathogen critically requiring research and development of new antimicrobial strategies (4, 5). 48A. baumannii, a gram-negative coccobacillus, is a member of the ESKAPE group of pathogens, which are 49 prominent for causing frequent and hard-to-treat healthcare-associated infections (6). 50As a species, A. baumannii is highly resilient, and capable of surviving for months in biofilms on abiotic 51 surfaces (7, 8). It can cause pneumonia, bacteremia, urinary tract infections, meningitis and wound infections, 52 particularly in the context of intensive care units, and is frequently associated with indwelling med...

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“…Data analysis was performed by the Monash Bioinformatics Platform (Monash University) using the P. gingivalis W83 NCBI reference sequence NC_002950.2 [26]. Raw RNAseq FASTQ files were aligned with the BWA-MEM aligner and analyzed using the RNAsik pipeline to generate raw counts [27]. Then, Degust was used for differential gene expression analysis and visualization [28].…”

Section: Differential Gene Expressionmentioning

confidence: 99%

Metabolic cooperativity between Porphyromonas gingivalis and Treponema denticola

Kin

Butler

Slakeski

et al. 2020

Journal of Oral Microbiology

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Background: Porphyromonas gingivalis and Treponema denticola are proteolytic periodontopathogens that co-localize in polymicrobial subgingival plaque biofilms, display in vitro growth symbiosis and synergistic virulence in animal models of disease. These symbioses are underpinned by a range of metabolic interactions including cooperative hydrolysis of glycine-containing peptides to produce free glycine, which T. denticola uses as a major energy and carbon source. Objective: To characterize the P. gingivalis gene products essential for these interactions. Methods: The P. gingivalis transcriptome exposed to cell-free T. denticola conditioned medium was determined using RNA-seq. P. gingivalis proteases potentially involved in hydrolysis of glycine-containing peptides were identified using a bioinformatics approach. Results: One hundred and thirty-twogenes displayed differential expression, with the pattern of gene expression consistent with succinate cross-feeding from T. denticola to P. gingivalis and metabolic shifts in the P. gingivalis folate-mediated one carbon superpathway. Interestingly, no P. gingivalis proteases were significantly up-regulated. Three P. gingivalis proteases were identified as candidates and inactivated to determine their role in the release of free glycine. P. gingivalis PG0753 and PG1788 but not PG1605 are involved in the hydrolysis of glycine-containing peptides, making free glycine available for T. denticola utilization. Conclusion: Collectively these metabolic interactions help to partition resources and engage synergistic interactions between these two species.

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RNAsik: A Pipeline for complete and reproducible RNA-seq analysis that runs anywhere with speed and ease

Cited by 45 publications

References 11 publications

Urban air particulate matter induces mitochondrial dysfunction in human olfactory mucosal cells

Urban air particulate matter induces mitochondrial dysfunction in human olfactory mucosal cells

Bacteriophages targeting Acinetobacter baumannii capsule induce antimicrobial resensitization

Metabolic cooperativity between Porphyromonas gingivalis and Treponema denticola

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