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Our NERC funded project on Antarctic Krill with @NHM_Science starts today! See details here nhm.ac.uk/discover/news/2024…
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Our latest study developing a Snakemake framework for the assembly and phylogenetic analysis of mitochondrial and ribosomal sequences from genome skims of museum collections is now published in @molecology with @NHM_Science onlinelibrary.wiley.com/doi/…
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🚨Job Alert: Are you a bioinformatics geek? familiar with ancient/historical DNA data? Do you want to join Kew Mycology to analyse fungal genomes of very old specimens? check our vacancies! careers.kew.org/vacancy/bioi…
careers.kew.org/vacancy/seni… #fungal #genomics #museomics
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Excited to share the final chapter of my PhD thesis has been published! 🎉 Country-wide DNA metabarcoding is now a reality, thanks to key advancements. Big thanks to my co-authors and all who supported me! @leeselab @Senckenberg Link: onlinelibrary.wiley.com/doi/…
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🚨 EntoSieve: New automated tool for fast, accurate size-sorting of bulk insect samples! Perfect for boosting DNA megabarcoding & metabarcoding projects. 🧬🔬 DIY low-cost device, gentle on specimens and yet efficient 🦋🐞read here: authorea.com/users/836612/ar…
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Are you attending #iBOL2024? Did you want to learn more about barcoding with nanopores?
Register to attend the pre-conference workshop. Space is limited!
dnabarcodingconference.com
@eZakhar0v @ento_ben @Elza74649502 @CBG_UofG
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OPPORTUNITY! We are recruiting an exceptional leader for NHM Collections:
Director of Collections: You'll lead a dedicated team, spearhead strategy for the future of collections, drive access and research, and ensure success of our multi-site expansion
nature.com/naturecareers/job…
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🚨 Job Alert! 🚨 Naturalis is hiring two tenure-track researchers. We're looking for experts who want to integrate molecular techniques, imaging, and data science (AI) to advance species recognition and detection. Apply here: naturalis.nl/en/about-us/job…. #Biodiversity #metabarcoding
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Replying to @eggrandio
If you want something super simple and reasonably priced, microCLEAN may be worth trying: microzone.co.uk/shop/post-am… (I would love to know how it works in terms of chemistry!).
Or you could try a cheap magnetic bead cleanup with reagents and magnet rack, possibly cheapest and most accessible from sergilabsupplies.com/product… haven’t tested these myself though).
If you want something very inexpensive but more time consuming and have enough samples to warrant stocking up on PEG, salt, and ethanol, a PEG precipitation may be useful, e.g.: sites.lsa.umich.edu/olsen-la… .
You could also try a freeze-and-squeeze extraction method extracting from TAE gels, e.g. xitter.cf/theBentoLab/status/173…
There will also be other methods, e.g. homemade spin columns, bought spin columns with homemade reagents, etc.
The question of which method would work best for you will probably depend on your own preferred balance of cost/speed/scalability/yield/reliability!
Hope that helps!
For anyone extracting PCR products from agarose gels (or who would like the option to do so occasionally), here’s a cheap and rapid homemade spin-column gel extraction method that’s reportedly good enough for Sanger sequencing without further purification.
The method, described by Abraham et al. (2017), is based on the observation that low concentrations of TAE (Tris-acetic acid-EDTA) buffer do not seem to inhibit PCR and Sanger sequencing. This means that a quick centrifugation of a gel slice through a filter could be enough to produce sequencing-ready DNA.
The authors made homemade spin columns by placing a small amount of cotton fiber (moistened with 0.5x TAE buffer), in a 0.5 mL centrifuge tube, and poked a hole in the bottom of the tube. This tube was then placed inside a 1.5 mL tube, and was then ready for use.
An electrophoresis gel was run using 0.5x TAE buffer, and successful amplicon bands cut out and placed in the homemade spin columns. The gel slices and columns were then centrifuged at 5200×g for 5 minutes to produce an extract used for Sanger sequencing reactions.
The authors reported a slight reduction in DNA yield compared to commercial gel extraction kits, but this didn’t impact results and their method was much cheaper and quicker. However, they did suggest that it’s best used for strong PCR bands, and it may not be quite as efficient as methods that totally remove TAE buffer. Their article can be found here:
Abraham et al. (2017). A quick and effective in-house method of DNA purification from agarose gel, suitable for sequencing. 3 Biotech, 7, 1-6.
ncbi.nlm.nih.gov/pmc/article…
Interestingly, this method appears to be a hybrid of the classic “freeze-and-squeeze” method (where the agarose is frozen before centrifugation to extract DNA), for example as described by Tautz & Renz (1983)...
Tautz & Renz (1983). An optimized freeze-squeeze method for the recovery of DNA fragments from agarose gels. Analytical biochemistry, 132(1), 14-19.
sciencedirect.com/science/ar… (subscription access).
… and Millipore’s Montage(TM) DNA Gel Extraction Kit, which uses proprietary filter columns plus a gel shredder to improve extraction efficiency without freezing. See Leonard et al. (1998) below for a description of the method using what is presumably a previous iteration of this kit:
Leonard et al. (1998). Preparation of PCR products for DNA sequencing. Biotechniques, 24(2), 314-317.
future-science.com/doi/abs/1…
Looking at all three protocols, two additional modifications to Abraham et al. (2017)'s method spring to mind:
⭐Replace the homemade spin column with a cut-down filter-pipette tip, making the method even cheaper and more accessible. You can find a great video by Rahul Patharkar on using filter-tip freeze-and-squeeze here: youtube.com/watch?v=b3wfhofZ… !
⭐Reduce the EDTA concentration in the TAE buffer to 1/10 of its normal concentration, in-line with Millipore’s Montage(TM) DNA Gel Extraction Kit recommendations.
In other words, you could try running a gel in a low EDTA TAE buffer to visualise amplicons, cut out gel bands, and centrifuge through filter tips to extract a (hopefully) Sanger sequencing-ready DNA extract.
As a disclaimer, Abraham et al. (2017) and Leonard et al. (1998) both used ethidium bromide in their gels. Other DNA stains might (or might not) have more of an impact on sequencing quality.
Also, if you do try it, I would also suggest testing on only a few samples to begin with just in case of failures!
And if you already use this method, or something similar, we'd love to know how works for you!
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Just updated BOLDigger2: By popular demand 🫡, BOLDigger2 now accepts BOLD credentials as optional arguments for seamless integration into existing bioinformatics pipelines. Update now at github.com/DominikBuchner/BO…! #boldigger2 #update 💻
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🚀 Excited to announce BOLDigger2! 🎉 Top 100 hits, better error handling, pipeline integration, faster downloads, tons of bug fixes, and BIN support. Check it out and feel free to share: github.com/DominikBuchner/BO… #BOLDigger2 #upscaling @leeselab
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How to efficiently implement #ONT for #DNAbarcoding applications? Join our webinar on June 6th to hear useful tips and discuss with experts from the @iBOLEurope community!
iboleurope.org/june-6th-webi…
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We’re sequencing the genomes of 10 endangered species with ORG.one live at London Calling! 🦁🦛🐛🐧🦆🐆🦌
Thanks to @NHM_London and @rzss for making this possible and helping to generate useful genomic data to support conservation efforts! #nanoporeconf
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Earlier today Heather Ritchie-Parker told us about how her team at the Royal Zoological Society of Scotland have been working with ORG. one to assemble reference genomes and inform conservation strategies #nanoporeconf
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Today is #BiodiversityDay2024! 🌍
An important day, as time is running out.
#BGE is scaling up the use of genomics to enhance understanding of biodiversity and guide interventions to address the #BiodiversityCrisis.
▶️Learn more: biodiversitygenomics.eu/know…
@REA_research #DNA
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Welcome to London ! At #nanoporeconf this year we will be live sequencing 10 Endangered and Critically Endangered Species to coincide with 10 years of London Calling. All supported through our ORG.one programme. Please come speak to us about it @nanopore
Ben Price retweeted
It's #EndangeredSpeciesDay! Celebrating the @nanopore ORG.one community's efforts to support conservation 🌍
Next week, we'll sequence 10 more species live at #nanoporeconf with @NHM_London and @rzss - join us at the Showcase stage on Tuesday! 🧬🦜🦋🦛🧬
Ben Price retweeted
The 2024 #Biodiversity #Genomics #Europe Barcoding Hackathon video is released! 🧬
But what is a hackathon, actually? And what topics did they work on? Watch this new interview video to find out more!💡
👉Go to: youtube.com/watch?v=HkA7lf5T…
@REA_research @iBOLEurope @erga_biodiv
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Here’s a novel and very clever method to detect specific amplicons produced by multiplex PCR in around 15 minutes using the naked eye, with no electrical power or gel electrophoresis.
It should be suitable for any multiplex PCR and is very scalable, so it could be useful for many different on-site nucleic acid testing needs, for example anything from fungal pathogen testing, to mosquito species detection, to point-of need health care testing.
The method, by Nakano et al. (2024), uses a rapid 4-step process:
⭐Run a multiplex PCR for a specific group of targets using primers modified with hybridisation tag sequences
⭐Incubate the PCR product with paramagnetic microbeads and a single hybridisation probe that allows selective attachment of one of the amplicons to the microbeads
⭐Wash the beads and resuspend them in distilled water
⭐Transfer 10 μL of each PCR to be tested for one target into round-bottomed wells of a blood coagulation reaction plate that is treated to make it hydrophilic, and put a 5 mm neodymium magnet under each well.
Positive results are seen as a single very dense black spot in the middle of the well, and negative results as a diffuse light patch — very easy to interpret!
But how and why does it work?
The answer is that when magnetic beads that have failed to hybridise to DNA fragments are placed over a strong magnet, the beads are attracted to the bottom of the wells and spread out due to the hydrophilic coating, forming a diffuse patch — a negative result.
However, if the magnetic beads have hybridised to DNA fragments, the DNA causes the beads to become hydrophobic instead of hydrophilic. When the beads are magnetised they're pulled to the bottom of the well by the magnet, but are also repelled by the bottom of the well and the water itself. The combination of attractive and repulsive forces causes the beads to cluster together in a very dense and easily detectable spot where the magnetic field is strongest — a positive result.
This method looks like it has some useful advantages over other rapid nucleic acid tests, such as LAMP (much simpler primer design), gel electrophoresis (faster, less power needed, simpler to interpret, higher throughput), and lateral flow strips (more flexible and scalable).
However, the authors haven't yet addressed issues of sensitivity of detection and the number of detectable targets in a multiplex PCR — these will be investigated in future studies.
A very clever method that looks like it might be very useful for many applications in the future!
You can read the article here:
Nakano et al. (2024). Selective visual detection of multiplex PCR amplicon using magnetic microbeads. Biosensors and Bioelectronics: X, 100461.
sciencedirect.com/science/ar…
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We welcome our latest acquisition to the curatorial team in the Small Orders! Diana Rendon Mera is a Colombian born #entomologist specialising in the diversity & systematics of Neotropical #Psyllidae (jumping plant lice). She has described over 50 new species from her studies!
























