The identification of nucleic acid aptamers would be advanced if they could be obtained after fewer rounds of selection and amplification. In this paper the identification of bivalent aptamers for thrombin by SELEX and single-step selection are compared using next generation sequencing and motif finding informatics. Results show that similar aptamers are identified by both methods. This is sign...

Aptamers are short nucleic acid sequences capable of specific, high-affinity molecular binding. They are isolated via SELEX (Systematic Evolution of Ligands by Exponential Enrichment), an evolutionary process that involves iterative rounds of selection and amplification before sequencing and aptamer characterization. As aptamers are genetic in nature, bioinformatic approaches have been used to ...

Culture-independent approaches, such as next-generation sequencing and microarray-based tools, provide insight into the identity and functional diversity of microbial communities. Although these approaches are potentially powerful tools in understanding microbial structure and function, there are a number of limitations that may bias conclusions. In order to mitigate these biases, an understand...

Formalin fixation followed by paraffin embedment (FFPE) is the most common method of preserving resected tissues. FFPEs can be easily stored, retrieved and processed for further analysis when compared to the logistical complications of processing fresh frozen (FF) material. Conversely, they may not be ideal for sequencing because of the nucleic acid fragmentation and artifacts introduced by fix...

Enzymes that move directionally on single-stranded nucleic acids are at the core of emerging nanopore sequencing technology. Of a particular use are DNA helicases, molecular motors that bind single-stranded DNA (ssDNA) independently of its sequence and use ATP to fuel their directional motion along the DNA (1). In nanopore-based sequencing, a pore formed by a protein channel embedded into a lip...

A thorough understanding of virus diversity in wildlife provides epidemiological baseline information about pathogens. In this study, eye swab samples were obtained from semi-domesticated reindeer (Rangifertarandus tarandus) in Norway during an outbreak of infectious eye disease, possibly a very early stage of infectious keratoconjunctivitis (IKC). Large scale molecular virus screening, based o...

To screen the nucleic acid aptamers of the EB virus-positive nasopharyngeal carcinoma cells, we used SELEX technology and synthesized in vitro a 78-nucleotide random DNA library. We used normal nasopharyngeal epithelial cells and EB virus-positive low differentiated nasopharyngeal carcinoma cells as target to conduct 10 cycles of screening, cloning, sequencing, and identification of the aptamer...

Background: Human Adenovirus species D (HAdV-D) was common human viral pathogen especially in eye infection, consists of several types of which HAdV-D8, -D19 and –D37 were common in eye infection. This study includes detection of HAdV-D types implicated in conjunctivitis based on L2 (Penton protein) gene similarity. Methods: Conjunctival swabs were collected from Keratoconjunctivitis patient...

BACKGROUND Different high-throughput nucleic acid sequencing platforms are currently available but a trade-off currently exists between the cost and number of reads that can be generated versus the read length that can be achieved. METHODOLOGY/PRINCIPAL FINDINGS We describe an experimental and computational pipeline yielding millions of reads that can exceed 200 bp with quality scores approac...

The emergence and re-emergence of various viral diseases indicate the need for the development of effective and authentic new diagnostic methods. The diagnostic application of gel-based PCR, general PCR systems, phylogeny, molecular epidemiology, real-time PCR, amplification without thermo-cycling, multiplex PCR, nucleic acid extraction and pipetting robotics, automation and quality control, in...