That's amazing. Do you have more videos illustrating the steps exactly of sample processing, data analysis?? Or if you can guide me to a good website plz. thanks
Incredible work. Hopefully the data folks like these collect are of good enough quality to actually be put into practical use when the situation is actually dire in the future.
Great video! I'm excited to see how much faster and easier DNA barcoding in the field will be 10 to 20 years from now. Hopefully the Ecuadorian members of Tropical Herping will stop by Mashpi during my internship over the summer. I'd love to help them out and learn some more photography tips!
Less than 10-20 years - more like the next couple of years! Next generation sequencing has been moving along so quickly, really exciting to see the future of portable sequencing. You should definitely sync up with the guys from TH
Awesome, that's perfect news for up-and-coming field biologists and entomologists! I'll definitely contact the TH guys before going. If you've got time some day, It'd be great to ask you a few questions (on Instagram or whatever works best) about my project in Mashpi and about college/career paths before I go back to Ecuador, because I do need a little guidance.
@@NextGenScientistDiscover Hey, I was curious if there is something new like minion or a better version out there? And can one sequence a whole human genome with it soon? Thx :)
You bring up a good point - one of the powerful features of nanopore is that it can sequence native DNA or RNA. However, there is trade-off with computational power, multiplexing samples, and time - and what you want to sequence really depends on your research question. If we want to rapidly identify species while in the field, and pool lots of individual on to one flow cell, then it may not be ideal to try and sequence native genomic DNA, but rather focus on specific loci. This is why did performed PCR on genes that are used for species identification; this allowed us to pool lots of samples, quickly sequence them, and using a laptop had enough computational power to sort everything out bioinformatically.
How did you keep your pcr reactive on shape in the forest? I would be scare to leave my taq at room temperature for long time. Also, how did you recude contamination?
@@NextGenScientistDiscover what sort of primers you used sir? Like you might be aware of the species right doesn't it cause primer bias?? Losing the novel species
What species samples did you use for collecting DNA, did you also have a mini centrifuge, what portable wet lab steps did you have to take prior to using the MiniPCR and MiniIon nanopore?
Hi there, you can find more information about the lab setup in the publication - academic.oup.com/gigascience/article/7/4/giy033/4958980. We brought out a mini centrifuge and mini PCR machine as well. All wet lab steps can be carried out in the field. A more recent preprint using long range PCR on plant, fungi and arthropod samples can be found here www.biorxiv.org/content/early/2018/06/29/358572
Radical! Similarly interested in such testing when I go to a remote village bordering DRC in Rwanda, understanding disparities in larvae in various still water areas. I will most certainly check out your links. Exciting, I am now already reading your specific details including the number of flow cells you took along, very nice!
@@raananikar Awesome! Please let me know if I can help answer any q's. For this trip just used one starter pack, and have helped with several other ONT projects at Berkeley.
While nanopore does have a relatively high raw error rate, there are many publications demonstrating how you can still create highly accurate consensus sequences, in particular for dual-indexed amplicons. Here's a short list of recent pubs: www.mdpi.com/2073-4425/11/10/1121, pubmed.ncbi.nlm.nih.gov/29617771/, academic.oup.com/gigascience/article/8/5/giz006/5368330, bmcbiol.biomedcentral.com/articles/10.1186/s12915-019-0706-9
That's amazing. Do you have more videos illustrating the steps exactly of sample processing, data analysis?? Or if you can guide me to a good website plz. thanks
Incredible work. Hopefully the data folks like these collect are of good enough quality to actually be put into practical use when the situation is actually dire in the future.
Great video! I'm excited to see how much faster and easier DNA barcoding in the field will be 10 to 20 years from now. Hopefully the Ecuadorian members of Tropical Herping will stop by Mashpi during my internship over the summer. I'd love to help them out and learn some more photography tips!
Less than 10-20 years - more like the next couple of years! Next generation sequencing has been moving along so quickly, really exciting to see the future of portable sequencing. You should definitely sync up with the guys from TH
Awesome, that's perfect news for up-and-coming field biologists and entomologists! I'll definitely contact the TH guys before going. If you've got time some day, It'd be great to ask you a few questions (on Instagram or whatever works best) about my project in Mashpi and about college/career paths before I go back to Ecuador, because I do need a little guidance.
Andy Better sure I'd be happy to chat sometime, feel free to send a DM
@@NextGenScientistDiscover Hey, I was curious if there is something new like minion or a better version out there? And can one sequence a whole human genome with it soon? Thx :)
Hmmm.... Coool.... But why mini PCR for nano pore sequencing ?
That’s awesome, so much faster!
Yes it was really exciting! Looking forward to future projects applying the portable lab in the field
Amazing work. Do you perform the data analysis/bioinformatics yourself?
why a miniPCR ? one of the purpose of nanapore (in addition with the miniaturization) is the fact that there is no need to amplify the signal right ?
You bring up a good point - one of the powerful features of nanopore is that it can sequence native DNA or RNA. However, there is trade-off with computational power, multiplexing samples, and time - and what you want to sequence really depends on your research question. If we want to rapidly identify species while in the field, and pool lots of individual on to one flow cell, then it may not be ideal to try and sequence native genomic DNA, but rather focus on specific loci. This is why did performed PCR on genes that are used for species identification; this allowed us to pool lots of samples, quickly sequence them, and using a laptop had enough computational power to sort everything out bioinformatically.
Thanks for the answer. [French student here]
How did you keep your pcr reactive on shape in the forest? I would be scare to leave my taq at room temperature for long time. Also, how did you recude contamination?
@@NextGenScientistDiscover what sort of primers you used sir? Like you might be aware of the species right doesn't it cause primer bias?? Losing the novel species
I am a clinical microbiologist from Myanmar. I am planning to buy the same set for my fungal sequencing project.
Can you get results for viruses or bacteria?
What species samples did you use for collecting DNA, did you also have a mini centrifuge, what portable wet lab steps did you have to take prior to using the MiniPCR and MiniIon nanopore?
Hi there, you can find more information about the lab setup in the publication - academic.oup.com/gigascience/article/7/4/giy033/4958980. We brought out a mini centrifuge and mini PCR machine as well. All wet lab steps can be carried out in the field. A more recent preprint using long range PCR on plant, fungi and arthropod samples can be found here www.biorxiv.org/content/early/2018/06/29/358572
Radical! Similarly interested in such testing when I go to a remote village bordering DRC in Rwanda, understanding disparities in larvae in various still water areas. I will most certainly check out your links. Exciting, I am now already reading your specific details including the number of flow cells you took along, very nice!
@@raananikar Awesome! Please let me know if I can help answer any q's. For this trip just used one starter pack, and have helped with several other ONT projects at Berkeley.
It is amazing! Fast ! How much analysis one sample cost?
Muchas gracias, soy de Ecuador, algun dia aspiro a este tipo de conocimiento. Saludos
No aspires! Arregla tus maletas y sal del paìs para poder obtenerlos! Saludos :D
That moment when you kind of decide you want to be biologist
Joan then my work here is done
Such dedication lolol
@@SoilStainedShirt I'm majoring in biochem now 🥺😭😭
Soo cool!
Sir, i want to join as your intern... Please help..
But what about the error rate of nano pore!!! Did you check the quality of your bases
While nanopore does have a relatively high raw error rate, there are many publications demonstrating how you can still create highly accurate consensus sequences, in particular for dual-indexed amplicons. Here's a short list of recent pubs: www.mdpi.com/2073-4425/11/10/1121, pubmed.ncbi.nlm.nih.gov/29617771/, academic.oup.com/gigascience/article/8/5/giz006/5368330, bmcbiol.biomedcentral.com/articles/10.1186/s12915-019-0706-9
@@NextGenScientistDiscover that's really nice of you thank you!! Waiting for more of your videos
Does anyone know which program is being used at 1:54?
The program is Geneious www.geneious.com/
@@NextGenScientistDiscover Thanks for the super fast reply!
What type of laptop u took ?
Looks like a MacBook
I'm curious to know how much that tiny thing costs?
Also what is that?: 2:20
1000 usd
Wow, thats much cheaper than I would have expected.
@@labeboye993well damn
Biopiratas en ecuador....
Western scientists helping understand national biodiversity, same as for last 400 years.
Fake video, no useful information