Search results for "Deep sequencing"
showing 8 items of 28 documents
AP5Z1/SPG4 8 frequency in autosomal recessive and sporadic spastic paraplegia
2014
Hereditary spastic paraplegias (HSP) constitute a rare and highly heterogeneous group of neurodegenerative disorders, defined clinically by progressive lower limb spasticity and pyramidal weakness. Autosomal recessive HSP as well as sporadic cases present a significant diagnostic challenge. Mutations in AP5Z1, a gene playing a role in intracellular membrane trafficking, have been recently reported to be associated with spastic paraplegia type 48 (SPG48). Our objective was to determine the relative frequency and clinical relevance of AP5Z1 mutations in a large cohort of 127 HSP patients. We applied a targeted next-generation sequencing approach to analyze all coding exons of the AP5Z1 gene. …
Direct squencing from the minimal number of DNA molecules needed to fill a 454 picotiterplate
2014
Notice of Republication: This article was republished on June 17, 2014, to correct an error in the title. The publisher apologizes for the error. In addition, a typographical error was corrected in the Abstract. Please download this article again to view the correct version. The originally published, uncorrected article and the republished, corrected article are provided here for reference.
High-throughput sequencing of RNA silencing-associated small RNAs in olive (Olea europaea L.).
2011
14 páginas, 5 figuras, 3 tablas, S4 figuras, S2 tablas
A genomic epidemiology investigation of yaws re-emergence and bacterial drug resistance selection
2020
Abstract Background In a longitudinal study assessing the WHO strategy for yaws eradication using mass azithromycin treatment, we observed resurgence of yaws cases with dominance of a single JG8 sequence type and emergence of azithromycin-resistant Treponema pallidum. Here, we analyse genomic changes in the bacterial population using samples collected during the study. Methods We performed whole bacterial genome sequencing directly on DNA extracted from 37 lesion swabs collected from patients on Lihir Island, Papua New Guinea, between 2013 and 2016. We produced phylogenies and correlated these with temporo-spatial information to investigate the source of new cases and the emergence of five …
Mapping of 7-methylguanosine (m7G), 3-methylcytidine (m3C), dihydrouridine (D) and 5-hydroxycytidine (ho5C) RNA modifications by AlkAniline-Seq
2021
Precise and reliable mapping of modified nucleotides in RNA is a challenging task in epitranscriptomics analysis. Only deep sequencing-based methods are able to provide both, a single-nucleotide resolution and sufficient selectivity and sensitivity. A number of protocols employing specific chemical reagents to distinguish modified RNA nucleotides from canonical parental residues have already proven their performance. We developed a deep-sequencing analytical pipeline for simultaneous detection of several modified nucleotides of different nature (methylation, hydroxylation, reduction) in RNA. The AlkAniline-Seq protocol uses intrinsic fragility of the N-glycosidic bond present in certain mod…
Analysis of pseudouridines and other RNA modifications using hydraPsiSeq protocol
2021
Detection of RNA modified nucleotides using deep sequencing can be performed by several approaches, including antibody-driven enrichment and natural or chemically induced RT signatures. However, only very few RNA modified nucleotides generate natural RT signatures and antibody-driven enrichment heavily depends on the quality of antibodies used and may be highly biased. Thus, the use of chemically-induced RT signatures is now considered as the most trusted experimental approach. In addition, the use of chemical reagents allows inclusion of simple "mock-treated" controls, to exclude spontaneous RT arrests, SNPs and other misincorporation-prone sites. Hydrazine is a well-known RNA-specific rea…
In vivophage display: identification of organ-specific peptides using deep sequencing and differential profiling across tissues
2020
ABSTRACTIn vivophage display is widely used for identification of organ- or disease-specific homing peptides. However, the currentin vivophage biopanning approaches fail to assess biodistribution of specific peptide phages across tissues during the screen, thus necessitating laborious and time-consuming post-screening validation studies on individual peptide phages. Here, we adopted bioinformatics tools used for RNA sequencing for analysis of high throughput sequencing (HTS) data to estimate the representation of individual peptides during biopanningin vivo. The data fromin vivophage screen were analyzed using differential binding – relative representation of each peptide in the target orga…
Experimental Evolution Reveals a Genetic Basis for Membrane-Associated Virus Release
2021
Many animal viruses replicate and are released from cells in close association to membranes. However, whether this is a passive process or is controlled by the virus remains poorly understood. Importantly, the genetic basis and evolvability of membrane-associated viral shedding have not been investigated. To address this, we performed a directed evolution experiment using coxsackievirus B3, a model enterovirus, in which we repeatedly selected the free-virion or the fast-sedimenting membrane-associated viral subpopulations. The virus responded to this selection regime by reproducibly fixing a series of mutations that altered the extent of membrane-associated viral shedding, as revealed by fu…