scholarly journals Oxford Nanopore sequencing in a research-based undergraduate course

2017 ◽  
Author(s):  
Yi Zeng ◽  
Christopher H. Martin
Keyword(s):  
Real Time ◽  
Learning Experience ◽  
Nanopore Sequencing ◽  
New Techniques ◽  
Undergraduate Biology ◽  
Novel Technologies ◽  
Biology Students ◽  
Oxford Nanopore ◽  
Sequencing Method ◽  
Excellent Tool

AbstractBackgroundNanopore sequencing is a third generation genomic sequencing method that offers real time sequencing of DNA samples. Nanopore sequencing is an excellent tool for teaching because it involves cutting-edge sequencing methods and also helps students to develop a research mindset, where students can learn to identify and resolve problems that arise during an experiment.ResultsWe, as a group of undergraduate biology students, were able to use nanopore sequencing to analyze a sample of pupfish DNA. We were able to accomplish this without computer science backgrounds and only some basic DNA extraction training. Although there were issues, such as inconsistent results across runs, we found it useful as a research learning experience and an application of the skills we learned.ConclusionsAs students, it was exciting to be able to experience this technology first hand and apply what we learned in the classroom. Nanopore sequencing holds potential for DNA sequencing of large fragments in real time. It allows students to be acquainted with novel technologies and the theories behind them. However, as with all new techniques, it does not have the same established support, and when students run into difficulties while using nanopore sequencing, it is often difficult to identify what went wrong.

Investigating Issues in the Laboratory

2014 ◽  
Vol 76 (9) ◽  
pp. 609-614 ◽  
Author(s):  
Krissi M. Hewitt ◽  
Lori J. Kayes ◽  
David Hubert ◽  
Adam Chouinard
Keyword(s):  
Invasive Species ◽  
Animal Behavior ◽  
Population Biology ◽  
Learning Experience ◽  
Reform Initiatives ◽  
Undergraduate Biology ◽  
Biology Students ◽  
Invasive Crayfish ◽  
Recent Reform ◽  
Introductory Biology Course

Recent reform initiatives in undergraduate biology call for curricula that prepare students for dealing with real-world issues and making important links between science and society. In response to this call, we have developed an issues-based laboratory module that uses guided inquiry to integrate the concepts of animal behavior and population biology into an issue of both local and global relevance. The issue associated with this module is “What should be done about invasive crayfish?” Students investigate plausible reasons why crayfish are often successful invasive species through hypothesis testing, collection of behavioral data on live crayfish, and quantitative reasoning. Students also consider economic and environmental impacts of invasive species on local and global ecosystems. We implemented this module in a large introductory biology course and conducted survey research to evaluate the module’s potential to serve as an interesting and valuable learning experience for undergraduate biology students.

scholarly journals Robust long-read native DNA sequencing using the ONT CsgG Nanopore system

2017 ◽  
Vol 2 ◽  
pp. 23 ◽  
Author(s):  
Jean-Michel Carter ◽  
Shobbir Hussain
Keyword(s):  
Dna Sequencing ◽  
Cancer Cell Line ◽  
Read Length ◽  
Nanopore Sequencing ◽  
Computational Tools ◽  
Practical Applications ◽  
Oxford Nanopore ◽  
Sequencing Method ◽  
Long Read ◽  
Oxford Nanopore Technologies

Background: The ability to obtain long read lengths during DNA sequencing has several potentially important practical applications. Especially long read lengths have been reported using the Nanopore sequencing method, currently commercially available from Oxford Nanopore Technologies (ONT). However, early reports have demonstrated only limited levels of combined throughput and sequence accuracy. Recently, ONT released a new CsgG pore sequencing system as well as a 250b/s translocation chemistry with potential for improvements. Methods: We made use of such components on ONTs miniature ‘MinION’ device and sequenced native genomic DNA obtained from the near haploid cancer cell line HAP1. Analysis of our data was performed utilising recently described computational tools tailored for nanopore/long-read sequencing outputs, and here we present our key findings. Results: From a single sequencing run, we obtained ~240,000 high-quality mapped reads, comprising a total of ~2.3 billion bases. A mean read length of 9.6kb and an N50 of ~17kb was achieved, while sequences mapped to reference with a mean identity of 85%. Notably, we obtained ~68X coverage of the mitochondrial genome and were able to achieve a mean consensus identity of 99.8% for sequenced mtDNA reads. Conclusions: With improved sequencing chemistries already released and higher-throughput instruments in the pipeline, this early study suggests that ONT CsgG-based sequencing may be a useful option for potential practical long-read applications.

scholarly journals The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1478
Author(s):  
Harrison J. Lamb ◽  
Ben J. Hayes ◽  
Loan T. Nguyen ◽  
Elizabeth M. Ross
Keyword(s):  
Real Time ◽  
African Swine Fever ◽  
Preliminary Evidence ◽  
Eastern Africa ◽  
Future Application ◽  
Nanopore Sequencing ◽  
Rapid Diagnostics ◽  
Oxford Nanopore ◽  
Cassava Plant ◽  
High Base

Oxford Nanopore Technologies’ MinION has proven to be a valuable tool within human and microbial genetics. Its capacity to produce long reads in real time has opened up unique applications for portable sequencing. Examples include tracking the recent African swine fever outbreak in China and providing a diagnostic tool for disease in the cassava plant in Eastern Africa. Here we review the current applications of Oxford Nanopore sequencing in livestock, then focus on proposed applications in livestock agriculture for rapid diagnostics, base modification detection, reference genome assembly and genomic prediction. In particular, we propose a future application: ‘crush-side genotyping’ for real-time on-farm genotyping for extensive industries such as northern Australian beef production. An initial in silico experiment to assess the feasibility of crush-side genotyping demonstrated promising results. SNPs were called from simulated Nanopore data, that included the relatively high base call error rate that is characteristic of the data, and calling parameters were varied to understand the feasibility of SNP calling at low coverages in a heterozygous population. With optimised genotype calling parameters, over 85% of the 10,000 simulated SNPs were able to be correctly called with coverages as low as 6×. These results provide preliminary evidence that Oxford Nanopore sequencing has potential to be used for real-time SNP genotyping in extensive livestock operations.

scholarly journals Real-time demultiplexing Nanopore barcoded sequencing data with npBarcode

2017 ◽  
Author(s):  
Son Hoang Nguyen ◽  
Tania Duarte ◽  
Lachlan J. M. Coin ◽  
Minh Duc Cao
Keyword(s):  
Real Time ◽  
Nanopore Sequencing ◽  
Sequencing Data ◽  
Analysis Pipeline ◽  
Bioinformatic Tools ◽  
Oxford Nanopore ◽  
Pooled Sequencing ◽  
Cross Platform ◽  
Real Time Applications ◽  
Friendly Graphical User Interface

AbstractMotivationThe recently introduced barcoding protocol to Oxford Nanopore sequencing has increased the versatility of the technology. Several bioinformatic tools have been developed to demultiplex the barcoded reads, but none of them support the streaming analysis. This limits the use of pooled sequencing in real-time applications, which is one of the main advantages of the technology.ResultsWe introduced npBarcode, an open source and cross platform tool for barcode demultiplex in streaming fashion. npBarcode can be seamlessly integrated into a streaming analysis pipeline. The tool also provides a friendly graphical user interface through npReader, allowing the real-time visual monitoring of the sequencing progress of barcoded samples. We show that npBarcode achieves comparable accuracies to the other alternatives.AvailabilitynpBarcode is bundled in Japsa - a Java tools kit for genome analysis, and is freely available at https://github.com/hsnguyen/npBarcode.

scholarly journals Real-time DNA barcoding in a remote rainforest using nanopore sequencing

2017 ◽  
Author(s):  
Aaron Pomerantz ◽  
Nicolás Peñafiel ◽  
Alejandro Arteaga ◽  
Lucas Bustamante ◽  
Frank Pichardo ◽  
...  
Keyword(s):  
Real Time ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Pcr Amplification ◽  
Field Work ◽  
Sequence Information ◽  
Nanopore Sequencing ◽  
Consensus Sequences ◽  
Oxford Nanopore ◽  
Research Facilities

AbstractAdvancements in portable scientific instruments provide promising avenues to expedite field work in order to understand the diverse array of organisms that inhabit our planet. Here we tested the feasibility for in situ molecular analyses of endemic fauna using a portable laboratory fitting within a single backpack, in one of the world’s most imperiled biodiversity hotspots: the Ecuadorian Chocó rainforest. We utilized portable equipment, including the MinION DNA sequencer (Oxford Nanopore Technologies) and miniPCR (miniPCR), to perform DNA extraction, PCR amplification and real-time DNA barcode sequencing of reptile specimens in the field. We demonstrate that nanopore sequencing can be implemented in a remote tropical forest to quickly and accurately identify species using DNA barcoding, as we generated consensus sequences for species resolution with an accuracy of >99% in less than 24 hours after collecting specimens. In addition, we generated sequence information at Universidad Tecnológica Indoamérica in Quito for the recently re-discovered Jambato toad Atelopus ignescens, which was thought to be extinct for 28 years, a rare species of blind snake Trilepida guayaquilensis, and two undescribed species of Dipsas snakes. In this study we establish how mobile laboratories and nanopore sequencing can help to accelerate species identification in remote areas (especially for species that are difficult to diagnose based on characters of external morphology), be applied to local research facilities in developing countries, and rapidly generate information for species that are rare, endangered and undescribed, which can potentially aid in conservation efforts.

scholarly journals Visualizing Cancer: A Transdisciplinary Art and Biology Collaborative

2018 ◽  
Vol 11 (2) ◽  
pp. 1-10 ◽  
Author(s):  
Camilla McComb ◽  
Gretchen Otto ◽  
Deborah Omans ◽  
Jennifer Garvey ◽  
Philip J Smaldino
Keyword(s):  
Visual Art ◽  
Learning Experience ◽  
Collaborative Teams ◽  
Art Students ◽  
Undergraduate Biology ◽  
Biology Students ◽  
Visual Model ◽  
Scientific Accuracy ◽  
Thinking Processes ◽  
The University

It would be safe to say that nearly every student enrolled in college knows someone who has been impacted by cancer. After all, cancer killed nearly 8.2 million people worldwide in 2012 (World Cancer Report, 2014). Using this fact as the impetus for change we decided to make cancer the focus of a “transdisciplinary” (Marshall, 2014) collaborative effort to simulate a reciprocal-learning experience between undergraduate biology and visual art students attending a university in Southeastern Michigan. The goal of the 2015 project was to create an active and authentic collaboration utilizing the university visual art and biology curricula. By engaging and connecting scientific and artistic critical thinking processes, we wanted to know: Could we design a class structure that would enable collaborative teams of art and biology students to create a visual model that represents a hallmark of cancer designed so that the model could also stand alone on artistic merit? In other words, could cancer visualization be transformed into works worthy of gallery display while maintaining scientific accuracy? In this paper we discuss the planning, implementation, results, and impact this work has had upon the way we now envision transdisciplinary collaboration.

scholarly journals Developing an Interactive 3D Learning Experience to Help Students Understand Key Regulatory Processes Associated with Glycolysis

2018 ◽  
Vol 42 (1) ◽  
Author(s):  
Jacqueline Mason ◽  
Kevin Brennan ◽  
Samantha Bond ◽  
Leah Lebowicz
Keyword(s):  
Science Education ◽  
Learning Experience ◽  
Allosteric Regulation ◽  
Undergraduate Biology ◽  
Biology Students ◽  
Regulatory Processes ◽  
Biological Phenomena ◽  
Interactive 3D

Recent recommendations for undergraduate biologyinstruction emphasize teaching foundational biologicalprinciples and helping students transfer these principles tomore complex biological phenomena. These curricularendeavors can be facilitated by the incorporation ofinteractive visualization materials. The following researchproject was developed to explore whether a visualinteractive didactic tool could be developed to improvelearning outcomes for undergraduate biology students onthe topic of allosteric regulation within the context ofglycolysis. The results of this research could be beneficialfor improving the development of interactive applicationsfor science education.

scholarly journals Robust long-read native DNA sequencing using the ONT CsgG Nanopore system

2018 ◽  
Vol 2 ◽  
pp. 23 ◽  
Author(s):  
Jean-Michel Carter ◽  
Shobbir Hussain
Keyword(s):  
Dna Sequencing ◽  
Cancer Cell Line ◽  
Read Length ◽  
Nanopore Sequencing ◽  
Computational Tools ◽  
Practical Applications ◽  
Oxford Nanopore ◽  
Sequencing Method ◽  
Long Read ◽  
Oxford Nanopore Technologies

Background: The ability to obtain long read lengths during DNA sequencing has several potentially important practical applications. Especially long read lengths have been reported using the Nanopore sequencing method, currently commercially available from Oxford Nanopore Technologies (ONT). However, early reports have demonstrated only limited levels of combined throughput and sequence accuracy. Recently, ONT released a new CsgG pore sequencing system as well as a 250b/s translocation chemistry with potential for improvements. Methods: We made use of such components on ONTs miniature ‘MinION’ device and sequenced native genomic DNA obtained from the near haploid cancer cell line HAP1. Analysis of our data was performed utilising recently described computational tools tailored for nanopore/long-read sequencing outputs, and here we present our key findings. Results: From a single sequencing run, we obtained ~240,000 high-quality mapped reads, comprising a total of ~2.3 billion bases. A mean read length of 9.6kb and an N50 of ~17kb was achieved, while sequences mapped to reference with a mean identity of 85%. Notably, we obtained ~68X coverage of the mitochondrial genome and were able to achieve a mean consensus identity of 99.8% for sequenced mtDNA reads. Conclusions: With improved sequencing chemistries already released and higher-throughput instruments in the pipeline, this early study suggests that ONT CsgG-based sequencing may be a useful option for potential practical long-read applications with relevance to complex genomes.

scholarly journals Robust long-read native DNA sequencing using the ONT CsgG Nanopore system

2017 ◽  
Vol 2 ◽  
pp. 23 ◽  
Author(s):  
Jean-Michel Carter ◽  
Shobbir Hussain
Keyword(s):  
Dna Sequencing ◽  
Cancer Cell Line ◽  
Read Length ◽  
Nanopore Sequencing ◽  
Computational Tools ◽  
Practical Applications ◽  
Oxford Nanopore ◽  
Sequencing Method ◽  
Long Read ◽  
Oxford Nanopore Technologies

Background: The ability to obtain long read lengths during DNA sequencing has several potentially important practical applications. Especially long read lengths have been reported using the Nanopore sequencing method, currently commercially available from Oxford Nanopore Technologies (ONT). However, early reports have demonstrated only limited levels of combined throughput and sequence accuracy. Recently, ONT released a new CsgG pore sequencing system as well as a 250b/s translocation chemistry with potential for improvements. Methods: We made use of such components on ONTs miniature ‘MinION’ device and sequenced native genomic DNA obtained from the near haploid cancer cell line HAP1. Analysis of our data was performed utilising recently described computational tools tailored for nanopore/long-read sequencing outputs, and here we present our key findings. Results: From a single sequencing run, we obtained ~240,000 high-quality mapped reads, comprising a total of ~2.3 billion bases. A mean read length of 9.6kb and an N50 of ~17kb was achieved, while sequences mapped to reference with a mean identity of 85%. Notably, we obtained ~68X coverage of the mitochondrial genome and were able to achieve a mean consensus identity of 99.8% for sequenced mtDNA reads. Conclusions: With improved sequencing chemistries already released and higher-throughput instruments in the pipeline, this early study suggests that ONT CsgG-based sequencing may be a useful option for potential practical long-read applications with relevance to complex genomes.

Being Aware of Your Thinking: Examining Mindfulness and Metacognition in Undergraduate Biology Students

2016 ◽  
Author(s):  
Mikah J. Pritchard ◽  
Trisha A. Turner ◽  
Ellen L. Usher ◽  
Faith L. Jones
Keyword(s):  
Undergraduate Biology ◽  
Biology Students
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