#wildlifegenomics Lab #2

In November, we wrapped up the installation of a small but exciting laboratory for domestic samples obtained from the areas in and around Guadalajara, in the Jalisco district of Mexico. A little different than the previous efforts at field laboratories by FPI (which is actually a thing now!), this laboratory is miniature but extremely focused. The company that owns it does a large amount of screening for disease vectors for domestic animals and some human samples, but they have never ventured into the world of DNA testing.

We were tasked with taking a small portable setup into a temporary lab space to run the first tests for Leptospira, Babesia and Ehrlichia on some known positive samples. In these circumstances, a variety of things could go wrong – the primers could be uncooperative, the extraction procedure could yield low amounts of DNA, or the positives themselves could be finicky or undependable. But to our utter delight, we were able to successfully get positives to amplify for leptospira and babesia infected animals. The test was simple – a quick extraction, PCR and gel electrophoresis, but the sheer number of doors that opens for the area is by no means unremarkable.

Future foci include making the setup and tests entirely portable, so vets can take it with them to sample animals directly in the field during field visits. Real-time results can completely streamline the process for regulating outbreaks of diseases in domestic animals in the area.

We are also helping them choose more disease-causing agents to test for in the area, and helping them officially launch the laboratory.

The possibilities, as always, are endless.

And we didn’t even have to sequence any DNA!

When they are ready to launch officially, I’ll be happy to rave a little more about them.

 


Terms of Note:

Leptospirosis is a bacterial disease that affects humans and animals. It is caused by bacteria of the genus Leptospira. In humans, it can cause a wide range of symptoms, some of which may be mistaken for other diseases. Some infected persons, however, may have no symptoms at all. Without treatment, Leptospirosis can lead to kidney damage, meningitis (inflammation of the membrane around the brain and spinal cord), liver failure, respiratory distress, and even death. Source: CDC
Babesiosis is a malaria-like parasitic disease caused by infection with Babesia, a type of Apicomplexa.[1] Human babesiosis transmission via tick bite is most common in the Northeastern and Midwestern United States and parts of Europe, and sporadic throughout the rest of the world. It occurs in warm weather.[2] People can get infected with Babesia parasites by the bite of an infected tick, by getting a blood transfusion from an infected donor of blood products, or by congenital transmission (an infected mother to her baby). Source: Wikipedia
Ehrlichia is a genus of rickettsiales bacteria that is transmitted to vertebrates by ticks. These bacteria cause the Ehrlichiosis infection, which is considered zoonotic, because the main reservoirs for the disease are animals. Source: Wikipedia

Can you #Genomicsinthejungle?

In the late summer of 2018, I had the very great pleasure of conducting the first ever field course on genomics in the Amazon rainforest. We used rugged, field-friendly technology based at the Green Lab at IGFS in Peru, and Oxford Nanopore’s tiny sequencer – the MinION – to get from sample to sequence in a remarkably short period of time.

In total, we ran four experiments focused on 16s metagenomics, 18s metagenomics, ddRADSeq digests, and DNA barcoding. Our samples ranged from everything from primates to batflies, spanning all major terrestrial taxonomic orders. We worked with feces, blood, whole ectoparasites, and other insects, and plant samples.

The resulting publications will be co-written by all the students in this field course. See below, for a summary of one of the most rewarding teaching experiences of my lifetime.

I will be teaching this course again – once in India this winter, and again in Peru in the summer of 2019. Please see here for details!

(If the imagery below doesn’t display in your browser, click the link to explore).https://embed.wakelet.com/wakes/8651396b-e4c7-40dd-90da-e75b45da9235/grid

New Pub: Classification of producer characteristics in primate long calls using neural networks

Her findings are both methodologically and analytically intriguing. She used a novel machine learning model called an artificial neural network to condense the large number of measures taken on each vocalisation into a meaningful set that could then be used to see if each call encoded information about the call’s producer – either sex, age, or even individual identity.
Here is the paper’s abstract:
Primate long calls are high-amplitude vocalizations that can be critical in maintaining intragroup contact and intergroup spacing, and can encode abundant information about a call’s producer, such as age, sex, and individual identity. Long calls of the wild emperor (Saguinus imperator) and saddleback (Leontocebus weddelli) tamarins were tested for these identity signals using artificial neural networks, machine-learning models that reduce subjectivity in vocalization classification. To assess whether modelling could be streamlined by using only factors which were responsible for the majority of variation within networks, each series of networks was re-trained after implementing two methods of feature selection. First, networks were trained and run using only the subset of variables whose weights accounted for ≥50% of each original network’s variation, as identified by the networks themselves. In the second, only variables implemented by decision trees in predicting outcomes were used. Networks predicted dependent variables above chance (≥58.7% for sex, ≥69.2 for age class, and ≥38.8% for seven to eight individuals), but classification accuracy was not markedly improved by feature selection. Findings are discussed with regard to implications for future studies on identity signaling in vocalizations and streamlining of data analysis.
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Robakis, E., Watsa, M. and Erkenswick, G., 2018. Classification of producer characteristics in primate long calls using neural networks. The Journal of the Acoustical Society of America144(1), pp.344-353.

The Green Lab

What if you could collect a sample from an animal, bring it back to camp, and be looking at the entirety of its genome by the same time the next day? Well, we think you can at the Green Lab. We are proud to collaborate with Field Projects International and the Inkaterra Association in the creation of the Amazon’s first in-situ molecular genetics field laboratory that can go from sample to sequence in just 24 hours.

The lab is located at the Inkaterra Guides Field Station, about an hour downriver from Puerto Maldonado on the Madre de Dios River in southeastern Peru. The Green Lab is set to launch in July 2018 with the following capabilities:

Biological sample preparation and storage, including but not limited to hair, nail, blood, faeces, serum, tissues and urine.

 

Kit-based DNA extraction from faeces, hair, blood (FTA cards), nail, and other tissues.

 

PCR-based DNA amplification with primers of your choice. We can procure these for you.

 

Agarose gel electrophoresis for presence/absence screening. Real-time visualisation and photography of gel results.

 

DNA quantification using fluorometer assays with a Quantiflor system.

 

Real-time portable genetic sequencing with ultra-long read lengths using MinION technology. Multiplexing possible.

 

Access the laboratory to perform analyses yourself, or leave it to our on-site experts.

 

Export of samples to an external provider for short turnaround Sanger sequencing

 

Winter field courses

 

screenshot-2016-10-03-12-08-03Several of our research team alumni are involved in teaching field courses in Peru and India this winter.

Liz Maciag, a research assistant alumn from 2011, will be teaching mammalogy with a focus on primatology in Peru. Tim Paine, long-time board member and veteran instructor will be co-teaching a module on herpetology in Peru. Ben Lybarger, a former research assistant, will be the lead TA on this course. For more details or to apply, please see here.

Lab PI Dr. Watsa and senior researcher Gideon Erkenswick will be teaching a course on primates and predators in the Western Ghats of India. They are joined by 2012 research assistant KC Hill, who is an expert on carnivore ecology and training to be a wildlife veterinarian today. For more details or to apply, please see here.

For a full listing of course offerings by FPI, please see here.

A new publication

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Our capture protocol is finally out! The journal Neotropical Primates has published our paper on novel handling methods of small arboreal primates. This was a collaborative effort including students who participated in our research program from its very inception in 2009. We are grateful for their perseverance, dedication and patience through this process!

For a photoessay on our mark-recapture program, or to participate in our global survey of primate protocols used in the last 20 years, please visit this page.