Quasispecies Analyses of the HIV-1 Near-full-length Genome with Illumina MiSeq
Frontiers in Microbiology, 2015 Human immunodeficiency virus type-1 (HIV-1) exhibits high between-host genetic diversity and within-host heterogeneity, recognized as quasispecies. Because HIV-1 quasispecies fluctuate in terms of multiple factors, such as antiretroviral exposure and ...
Hirotaka eOde +10 more
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Aromatic plants, nest bacterial diversity, and nestling condition in Corsican blue tits
Oikos, EarlyView.According to the ‘nest protection hypothesis', some passerines incorporate fresh aromatic plants into their nests which reduce pathogens that can negatively affect nestlings. We experimentally evaluated the effect of five aromatic plant species on the nest bacterial microbiota of Corsican blue tits Cyanistes caeruleus.
Hélène Dion‐Phénix +5 more
wiley +1 more source
GenomeTrakr WGS Protocol Collection and Workflow for MiSeq v2
, 2022 Here we have created a collection of all the protocols used for WGS using the MiSeq, in order, from sample extraction to NCBI submission. This collection has three sections: Section 1: WGS Wet lab workflow for Illumina MiSeq Section 2: Dry lab workflow for sequence QC and NCBI submission - Direct Submission Section 3: Dry lab workflow for sequence ...
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A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine [PDF]
, 2017 Avian H9N2 and 2009 pandemic H1N1 (pH1N1) influenza viruses can infect pigs and humans, raising the concern that H9N2: pH1N1 reassortant viruses could emerge.
Ma, Wenjun +5 more
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Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform
PLOS ONE, 2017 Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq.
Chongqing Wen +10 more
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PLANTS, PEOPLE, PLANET, EarlyView.Trees in cities provide a great number of benefits to people and nature, but they are challenged by harsh conditions. Trees rely on helpful fungi in their roots to get essential nutrients from the soil, but we do not know which of these fungi are resistant to city landscapes.
Casper T. Verbeek +2 more
wiley +1 more source
MaxSSmap: A GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence [PDF]
, 2014 Programs based on hash tables and Burrows-Wheeler are very fast for mapping short reads to genomes but have low accuracy in the presence of mismatches and gaps.
Roshan, Usman, Turki, Turki
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16S Sequencing on Illumina MiSeq Platform v1
The 16S protocol detailed here is designed to amplify bacteria using V4-V5 hyper-variable regions of the 16S rRNA gene on the Illumina MiSeq DNA sequencer.
Angela Schmoldt, Melissa Schussman
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Azole antifungal contaminants disrupt mycorrhizal function and risk agricultural sustainability
PLANTS, PEOPLE, PLANET, EarlyView.Global food production is increasingly threatened by soil degradation, climate change and the rising costs of synthetic fertilisers. Circular agriculture, which promotes resource reuse, is a promising solution, but using treated wastewater and biosolids in farming introduces risks from emerging contaminants like pharmaceutical residues.
Emily K. Durant +5 more
wiley +1 more source
Exploration of the Neuronal Subtype Specificity of an Ethanol Responsive Gene: Glycogen Synthase Kinase 3 Beta (Gsk3b) [PDF]
, 2020 Exploration of the Neuronal Subtype Specificity of an Ethanol Responsive Gene: Glycogen Synthase Kinase 3 Beta (Gsk3b) Dalton Huey, Depts. of Bioinformatics, Biology & Chemistry, A. van der Vaart, G. M. Harris, and M. F. Miles, with Dr.
Harris, G M +3 more
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