Barcoding; Field and Lab Management Information Systems

Informatics  samples

International Centre of Insect Physiology and Ecology (ICIPE) hosted a group of trainers from Consortium of Barcode of Life (CBOL) and fifteen scientists to learn DNA Barcode of Wildlife Informatics. The elements of this critical training were to introduce them to Geneious (a DNA alignment, assembly, and analysis software), Field Information Managements Systems (FIMS), and Laboratory Information Managements Systems (LIMS). The scientists were fetched from National Museums of Kenya (NMK), Kenya Wildlife Service (KWS), International Centre of Insect Physiology and Ecology (ICIPE), Kenya Agricultural Research Institute (KARI), and Institute of Primate Research (IPR).

DNA barcoding is a technique that uses short DNA sequences from standardized positions in the genome to identify species. The overall goal of the training is to bridge the gap between conservation genetics and law enforcement. Barcode of Wildlife Project has a big part to play in protection of Kenya’s biodiversity as well as curbing illegaly harvested plant materials, poached tusks, horns, and meat sold as bushmeat.   Barcoding is a process of using DNA sequence to identify a specimen.

 

Dr Daniel Masiga, Head of the Molecular Biology Unit, ICIPE.

“It’s very difficult for wildlife authorities to determine whether a piece of meat has come from livestock or from wildlife, hence DNA barcording allows an institution like Kenya Wildlife Service to very quickly determine whether one is dealing with bushmeat or legal processed wildlife,” Dr Daniel Masiga, Senior Scientist and Head of the Molecular Biology Unit at ICIPE.

He said the project will greatly facilitate forensics in the protection of wildlife species, and in dealing with identifying cases of contamination both in wild animals and plants. Barcoding project keenly incorporates plants as well. “In Kenya today there is a growing market for ‘miti shamba’ (traditional medicine) some of which are packaged in capsules as medicinal products. Its extremely difficult for customers what is genuine from the not thus barcoding will help determine counterfeit from the originals.” Dr Masiga.

Informatics group discussions

Informatics helps to track samples as collected in the field all the way to the analysis and determination of what species have been identified. The initial stage involves building up of database of collected samples.

Informatics is really critical and is divided into two components. Field Information Managements Systems (FIMS) helps track the entire analytical flow of the entire chain of samples from the source species into the lab. Laboratory Information Managements Systems (LIMS) tracks the analytical flow within the lab generating the DNA extraction of samples all the way to sequencing and determining what the sequences. 

As the number of samples to the lab increase, tracking of samples and where they are stored is very important and the informatics takes care of that.

Video Conference with participants

Subsequently, it’s not only the issue of determining the number of specimens one has but also how that decision has been reached and linking with the specimens’ information which is held at FIMS.

Both Field Information Managements Systems and Laboratory Information Managements Systems are critical in the success of the barcode project, and enhances collaboration with other countries involved in the project.

Training Focuses on DNA Barcoding Processes

Participants pose for group photograph at BecA-ILRI Hub.

A group of trainers and twenty scientists assembled at the Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub for a week of training. DNA barcoding is a technique that uses short DNA sequences from standardized positions in the genome to identify species.

The modules of this training were DNA extraction, amplification, purification and sequencing of DNA from plant, animal tissue and blood samples, and understanding the processes involved in barcoding. 

The BecA-ILRI Hub focuses on the high-end biosciences that are complementary to capabilities already available in various national institutes and universities within the region.

These scientists, already producing lots of molecular data, are leaders in laboratory processing of molecular biological samples and were carefully selected from five different institutions; National Museums of Kenya, Kenya Wildlife Service,  International Centre of Insect Physiology and Ecology (ICIPE), Kenya Agricultural Research Institute (KARI), Government Chemist, and Institute of Primate Research.

Dr Niamh Redmond (3rd l) Barcoding Project manager CBOL during the training

During the training they focused on DNA barcording which is a highly standardized high quality data that the police and crime prosecutors can use to investigate wildlife crime, poaching, and trafficking of endangered species. Henceforth, the evidence brought to court must be of high quality.They focused on informatics and data management, and the lab procedures they will be using to get DNA sequences from plants and animal species.

BecA-ILRI Hub is a co-creation of the African Union's New Partnership for Africa's Development (AU/NEPAD) and ILRI. This shared research platform enables African science leaders to solve some of Africa's key agricultural challenges, through the applications of modern biotechnology. Its an exceptionally good laboratory and their major role in this particular training was capacity building.

Scientists were carefully selected from various institutions

"The Barcode of Wildlife Project is helping police and crime prosecutors in Kenya to catch criminals that are poaching and harvesting valuable species. The training will now raise the ability of Kenyan laboratories to the global scale hence becoming a global leader in fight against wildlife crime using the latest bio-technology," Dr. David Schindel, Executive Secretary of Consortium for the Barcode of Life Project said.

Barcode of Wildlife Project is working with six Partner Countries and its goals are to demonstrate use of DNA barcode evidence in investigations, prosecutions, convictions by November 2014, construct a reference BARCODE library to support Partner Country priorities, and for these partner countries to formally adopt, implement and fund barcoding.

The BecA-ILRI Hub has five core operational areas that include capacity building through research, research on key agricultural development priorities, technology platforms development and services, networking and institution strengthening, and product development and pathways to impact.Strengthening Agricultural Research in Eastern and Central Africa (ASARECA).

Additional sources: https://www.ilri.org/node/328, http://hub.africabiosciences.org/aboutbeca

Progress of DNA Barcode of Wildlife Informatics Training Workshop

Dr David Schindel, CBOL, gives an overview of DNA Barcode of Wildlife Informatics Training Workshop held at Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, in Kenya. The objective of the training is to provide lab training in the methods associated with the DNA barcoding pipeline. 

 Wide range of hands-on experience  

Specifically, participants will acquire skills in DNA extraction, amplification, purification and sequencing of plant, animal and blood samples. They are also gaining:
●  hands-on experience using a range of lab equipment and reagents
● experience working at different scales / sample sizes
● understanding of the processes involved in barcoding and how to deal with the different success rates and the properties of different markers.

Dr Dan Masiga, ICIPE, enlightens participants

Identification of trace evidence that can assist wildlife crime case by proving an offense has taken place, identifying an offender, linking an offender to both crime scene and items removed from a crime scene with that scene all form a critical part in compiling a case.

Through these experiences, DNA barcoding in Kenya will ultimately help prosecute wildlife criminals.

BoWPK’s Academics and Informatics Training Workshop

Esther Wangui; sample preparation at NMK

The Barcode of Wildlife Project Kenya (BoWPK) will hold its Academics and Informatics training Workshop  between 22^nd to 30^th April 2014. The objective of the workshop is to test the cost-effectiveness, scalability, and real-world impact of a DNA-based technology on the enforcement of species protection laws and treaties. 

During this period, animal samples from Kenya Wildlife Service (KWS) Forensic and Genetics Laboratory, and plants species from National Museums of Kenya (NMK) have been assembled to be used to isolate DNA for sequencing and subsequent preparation of DNA barcodes. 

The animal samples were isolated from healthy live animals collected from different parts of the country. Samples for DNA isolation were obtained from animals free from any observable infections. 

In the meantime, Consortium of Barcode of Life (CBOL) has prepared short introductory videos for each consultation and module introducing the training plan, BARCODE data standard and the extension of the standard that will be used in Barcode of Wildlife Project.

Sealed samples for the workshop

Informatics training workshop has been distributed into different modules; What is a Field Information Management System (FIMS) and FIMS spreadsheet?, Introduction and installation of Geneious, General Introduction to the Geneious software, Validating specimen data & uploading to FIMS, Importing specimen data from FIMS to LIMS, creating Extraction Plates, Creating PCR Plates, Creating Cycle Sequencing Plates, Cherry Picking, Editing Sequences, Sequence Analysis, and Uploading final data to GenBank.

Sealed samples for the workshop

Barcode of wildlife project is a collaborative project between National Museums of Kenya (NMK), Kenya wildlife Service (KWS), Consortium of Barcode of Life and Google. The project is designed as a proof-of-concept for ‘DNA barcoding’ as a system that would  be used in developing countries by border inspectors, park rangers and other regulatory officials to detect illegal trafficking in protected species.

The workshop will be held at both the laboratories facilities at the Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, 22-26 April for Academics Training,  and the International Centre of Insect Physiology and Ecology (ICIPE), an international scientific research institute, 28-30 April, for Informatics Training

John Kariuki, KWS; sample sealing

Dr Peris Kamau, NMK, during sample preparation

NMK Research Scientists Esther Wangui and Brenda Nyaboke cross check accuracy of collected samples.

Kenyatta 'Appalled' by Poaching Trade

President Uhuru Kenyatta has called on security agencies and wildlife authorities in the East African region to cooperate more closely in order to stem the rise of poaching incidents. 

President Uhuru Kenyatta

Kenyatta has raised concern over increased poaching incidences in the country henceforth issuing a stern notice. “The Government will not tolerate individuals focused on killing animals to create wealth. As members of the international community, and in line with our national values, we embrace the principles of sustainable development. Our economic well-being is strongly interrelated with our natural heritage. We believe that as we pursue development today, we should ensure that we do not compromise our future potential for development,” said Uhuru during his State of the Nation address.

Environment Cabinet Secretary Prof Judy Wakhungu has said her Ministry is investigating recent claims of a possible collusion between Kenya Wildlife Service ( KWS) rangers and poachers. Ms Wakhungu further said the Government will not declare poaching, mainly of elephants and rhinos as national disaster as some conservationists have demanded saying KWS is equal to the task of containing the vice. 

Prof Judy Wakhungu

Speaking during the Cabinet briefing, the Cabinet Secretary said although most of the wildlife handlers in the game parks were doing their best to contain the spiraling cases of poaching, some warders and rangers could be abetting the crime. She revealed that since 2009, 17 officers had been sacked for colluding with poachers, warning that they are also following some intelligence information on possible involvement of more rangers in the crime.

 “Since I came to office, we have interdicted 32 other officers, while others are suspended as we undertake investigations on collusion with poachers. We have solid information, which we are closely following in the fight against possible involvement of KWS rangers in this worrying vice,” she said. 

Ms Wakhungu has also expressed concern over rising cases of poaching in the country which now threatens tourism. “It’s unfortunate we lost a 3-year-old female white rhino at the park. This rhino was shot at 11pm on Thursday evening. Rangers responded and fought back the poachers before they could chop off the rhino horn,” she was speaking at Lake Nakuru National Park where poachers recently shot and killed a female rhino. 

Prof Wakhungu was accompanied by acting KWS director William Kiprono and other senior officers had visited the park moments after the outrageous incident. 

In the meantime, the Kenya Government and the United Nations have signed a development assistance framework that will see the UN mobilising KSh 102 billion for implementation of development programmes in the country over a four-year period. The President said decisions on pressing environmental challenges and opportunities will be made. “For reasons that should be evident, we await the High Level Dialogue on Illegal Wildlife Trade with the keenest interest.”