Oxford nanopore technology to address Tanzania’s wildlife conservation

11Jan 2021
Gerald Kitabu
Arusha
The Guardian
Oxford nanopore technology to address Tanzania’s wildlife conservation

​​​​​​​OXFORD Nanopore sequencing is a unique, novel and portable molecular technique that enables direct, real-time analysis of long DNA or RNA fragments. Our Correspondent Gerald Kitabu caught up with senior conservation officer-veterinary Tanzania National Parks (TANAPA) Dr. Emmanuel Macha-

-at portable genomics practical training using Oxford Nanopore technologies held at a the Arusha-based Nelson Mandela African Institution of Science and Technology (NM-AIST) recently. Excerpts;

QUESTION: Briefly tell us on how the technology works.

ANSWER: This technology is a unique, novel and portable molecular technique that enables direct, real-time analysis of long DNA or RNA fragments. The technology monitor changes to an electrical current as nucleic acids are passed through an ultra small pore with a nano dimension embedded in a protein membrane. The resulting signal is decoded to provide the specific DNA or RNA sequence by using artificial intelligence software.

Q: When was it founded?

A: This technology was founded in Oxford, United Kingdom in the year 2005 and officially launched at Butiama, Tanzania for the first time in  the world in 2014. The technology has vast application in the studies of diversity and evolution of living things. It has also been used in detection of pathogenic organisms thus useful in diseases diagnosis to both plants and animals.  Since its inception, the technology has been widely applied a genomic tool for sustainable management of emerging insect pests and diseases in crops as well as in the diagnosis of Ebola, Zika and during the recent COVID-19 pandemic.

Q: What is the advantage of this technology over others?

A: The advantage of this technology over others include:-Portability: Oxford Nanopore sequencer is portable, easy to use and can be used on farm/field tests. Actually, the sequencing machine itself can be carried in some ones pocket! The technology does not need a specialized building as a laboratory and anybody with a basic education can be trained and be able to use it.

Cost effective: The technology is relatively cost effective as it does not need a specialized training, usefulness on site, no dedicated laboratory building is needed and more so, it does need samples to be shipped outside the country for analyses. This saves a lot of time and money as well. 

Long reads: Oxford Nanopore sequencer gives long reads of sequences. This enables to have better assemblies, structural variants with a full length transcript. Therefore, by giving long reads, a full genome of an organism can be sequenced.

Very fast: The speed of this technology is very fast with no redundancy. It can analyze 450 samples per second. Data can be generated within 5 minutes.

Q: How can you apply to wildlife conservation and protection?

A: Oxford nanopore sequencing technologies has a wide application in wildlife on both conservation and protection. Some of the key areas that can be applied includes:-

First, DNA profiling of plants and animals: the technology as mentioned earlier can be used in diversity and evolutionary studies of living things. Currently, some of our national parks have been invaded by Alien Invasive plant species where the several methods including chemicals (herbicides) have been used to control. However, despite huge efforts that have been applied so far, these plants continue to be a challenge to habitats. This technology is bale to exactly identify the plant and give the correct herbicide or any other biological control method that can be used to manage it. More importantly also, some national parks are rich in endangered species some, some are critically endangered where their precious DNA need to be profiled. Examples of these animals are black rhinoceros, wild dogs and chimpanzee.  Therefore, genotyping them will enhance sound decisions with scientific evidence for their better management interventions, for example, avoiding poor genes due to inbreeding in some species.  This information is also important when deciding for translocation of various species with their specifics. 

Secondly, diseases diagnosis: Oxford nanopore technology can be used to detect pathogenic organisms to both plants and animals. During outbreak of notifiable diseases in wildlife (anthrax, rabies), the authorities use huge amount of money and resources in trying to control. One of major setback is the capacity to timely diagnose the underlying disease and thus delay to institute an appropriate control measure. Other conditions that have been affecting wildlife include; baboon genital disease, giraffe skin disease, giraffe ear disease, sitatunga and bushbuck deaths due to unknown disease. Because the capacity in country is inadequate; samples in most cases have been shipped to overseas for analyses. Shipping samples overseas cost money and time, therefore, a technology such as Oxford nanopore is of paramount important.

Thirdly, forensic investigation: Judges and magistrates before courts need exhibits that are beyond reasonable doubts in court cases involving wildlife. This technology, apart from identifying a plant or animal (even if it is a product), it can also tell the origin of it, therefore, adding more value and power in wildlife forensic investigation. For example, if a stockpile of rhinoceros horns or elephant ivories are confiscated, the technology can tell their origin.

 

Q: What are your commendations?

A: As human and wildlife population increases, their interactions also increase. This interaction increase the exposure and threat to emerging and re-emerging of zoonotic and other important diseases outbreak in wildlife and introduction of Alien Invasive Species (AIS). Therefore, a fast, real-time and a cost effective technology is needed to complement control efforts. Apparently, it is my feeling that, Oxford nanopore sequencing technologies to be the “cutting edge” molecular techniques that can be used by scientific and conservation communities in helping to solve the prevailing conservation challenges.  It is my hope that the technology will be accepted and adopted for use by conservation authorities (TANAPA, TAWIRI, NCAA, and TAWA), policy makers, scientists and other conservation stakeholders.

Lastly but not least, I would like to thank Tanzania Agriculture Research Institute (TARI) and NM-AIST for organising this training of trainers while hoping that the participants will impart this knowledge to other interested parties in their respective organisations.

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