BLAST: at the core of a powerful and diverse set of sequence analysis tools

McGinnis, Scott D.; Madden, Thomas

doi:10.1093/nar/gkh435

Cited by 1,706 publications

(1,265 citation statements)

References 11 publications

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“…We conducted BLASTx sequence similarity searches of the NCBI nonredundant protein database (downloaded Oct 21, 2016), Swissprot protein database (downloaded Oct 21, 2016) and the Ensembl human protein database (downloaded Oct 26, 2016) using NCBI BLAST 2.5.0 + (McGinnis & Madden, 2004) with an e‐value cutoff of 1E‐03 for transcript contigs identified as being differentially expressed (>2 fold change and FDR < 0.05) via the DESeq2 or edgeR analyses. We used the Ensembl human protein IDs identified in the DESeq2 or edgeR analyses as input for the web‐based g:Profiler (Reimand et al., 2016) to test for gene ontology (GO) term enrichment (Conesa et al., 2005), using a g:SCS significance threshold <0.05.…”

Section: Methodsmentioning

confidence: 99%

The other white‐nose syndrome transcriptome: Tolerant and susceptible hosts respond differently to the pathogen Pseudogymnoascus destructans

Davy

Donaldson

Willis

et al. 2017

Ecology and Evolution

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Mitigation of emerging infectious diseases that threaten global biodiversity requires an understanding of critical host and pathogen responses to infection. For multihost pathogens where pathogen virulence or host susceptibility is variable, host–pathogen interactions in tolerant species may identify potential avenues for adaptive evolution in recently exposed, susceptible hosts. For example, the fungus Pseudogymnoascus destructans causes white‐nose syndrome (WNS) in hibernating bats and is responsible for catastrophic declines in some species in North America, where it was recently introduced. Bats in Europe and Asia, where the pathogen is endemic, are only mildly affected. Different environmental conditions among Nearctic and Palearctic hibernacula have been proposed as an explanation for variable disease outcomes, but this hypothesis has not been experimentally tested. We report the first controlled, experimental investigation of response to P. destructans in a tolerant, European species of bat (the greater mouse‐eared bat, Myotis myotis). We compared body condition, disease outcomes and gene expression in control (sham‐exposed) and exposed M. myotis that hibernated under controlled environmental conditions following treatment. Tolerant M. myotis experienced extremely limited fungal growth and did not exhibit symptoms of WNS. However, we detected no differential expression of genes associated with immune response in exposed bats, indicating that immune response does not drive tolerance of P. destructans in late hibernation. Variable responses to P. destructans among bat species cannot be attributed solely to environmental or ecological factors. Instead, our results implicate coevolution with the pathogen, and highlight the dynamic nature of the “white‐nose syndrome transcriptome.” Interspecific variation in response to exposure by the host (and possibly pathogen) emphasizes the importance of context in studies of the bat‐WNS system, and robust characterization of genetic responses to exposure in various hosts and the pathogen should precede any attempts to use particular bat species as generalizable “model hosts.”

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Section: Methodsmentioning

confidence: 99%

The other white‐nose syndrome transcriptome: Tolerant and susceptible hosts respond differently to the pathogen Pseudogymnoascus destructans

Davy

Donaldson

Willis

et al. 2017

Ecology and Evolution

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“…DNA sequencing reactions were carried out by ServiceXS (Leiden, the Netherlands). Blast algorithms (McGinnis & Madden, 2004) were used to screen databases at the National Center for Biotechnology Information (NCBI) (Bethesda, MD, USA).…”

Section: Methodsmentioning

confidence: 99%

Specific protein homeostatic functions of small heat‐shock proteins increase lifespan

et al. 2015

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SummaryDuring aging, oxidized, misfolded, and aggregated proteins accumulate in cells, while the capacity to deal with protein damage declines severely. To cope with the toxicity of damaged proteins, cells rely on protein quality control networks, in particular proteins belonging to the family of heat‐shock proteins (HSPs). As safeguards of the cellular proteome, HSPs assist in protein folding and prevent accumulation of damaged, misfolded proteins. Here, we compared the capacity of all Drosophila melanogaster small HSP family members for their ability to assist in refolding stress‐denatured substrates and/or to prevent aggregation of disease‐associated misfolded proteins. We identified CG14207 as a novel and potent small HSP member that exclusively assisted in HSP70‐dependent refolding of stress‐denatured proteins. Furthermore, we report that HSP67BC, which has no role in protein refolding, was the most effective small HSP preventing toxic protein aggregation in an HSP70‐independent manner. Importantly, overexpression of both CG14207 and HSP67BC in Drosophila leads to a mild increase in lifespan, demonstrating that increased levels of functionally diverse small HSPs can promote longevity in vivo.

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“…DNA sequencing was performed by BMR Genomics srl (Italy, http://www.bmr-genomics.it). The obtained 16S rRNA sequences were aligned with the reference GenBank sequences using the BLASTN tool of the NCBI website (McGinnis and Madden, 2004). Phylogenetic relationships to known species were inferred by both the neighborejoining and the maximum likelihood methods using the software Mega6 (Tamura et al, 2013) with the aim to determine the most closely related specie.…”

Section: Colony Pcr Of Rdna 16s Gene Blast Alignment and Phylogenetimentioning

confidence: 99%

Bacterial community structure and removal performances in IFAS-MBRs: A pilot plant case study

Mannina

Capodici

Cosenza

et al. 2017

Journal of Environmental Management

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a b s t r a c tThe paper reports the results of an experimental campaign carried out on a University of Cape Town (UCT) integrated fixed-film activated sludge (IFAS) membrane bioreactor (MBR) pilot plant. The pilot plant was analysed in terms of chemical oxygen demand (COD) and nutrients removal, kinetic/stoichiometric parameters, membrane fouling and sludge dewaterability. Moreover, the cultivable bacterial community structure was also analysed.The pilot plant showed excellent COD removal efficiency throughout experiments, with average value higher than 98%, despite the slight variations of the influent wastewater. The achieved nitrification efficiency was close to 98% for most of the experiments, suggesting that the biofilm in the aerobic compartment might have sustained the complete nitrification of the influent ammonia, even for concentrations higher than 100 mg L À1 . The irreversible resistance due to superficial cake deposition was the mechanism that mostly affected the membrane fouling. Moreover, it was noticed an increase of the resistance due pore blocking likely due to the increase of the EPS Bound fraction that could derive by biofilm detachment.The bacterial strains isolated from aerobic tank are wastewater bacteria known for exhibiting efficient heterotrophic nitrificationeaerobic denitrification and producing biofilm.

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BLAST: at the core of a powerful and diverse set of sequence analysis tools

Cited by 1,706 publications

References 11 publications

The other white‐nose syndrome transcriptome: Tolerant and susceptible hosts respond differently to the pathogen Pseudogymnoascus destructans

The other white‐nose syndrome transcriptome: Tolerant and susceptible hosts respond differently to the pathogen Pseudogymnoascus destructans

Specific protein homeostatic functions of small heat‐shock proteins increase lifespan

Bacterial community structure and removal performances in IFAS-MBRs: A pilot plant case study

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