Bento Lab 🧬 @theBentoLab Twitter profile

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Bento Lab 🧬

@theBentoLab

7 months

Here’s an interesting PCR method for working with extremely low concentrations of DNA: “Booster PCR”. It looks like a rarely used and now obsolete method for most research, but it may be worth a try to give a PCR a boost if you can't access other more sensitive amplification or…

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Bento Lab 🧬

@theBentoLab

4 months

For anyone interested in teaching or learning PCR and DNA barcoding, here’s some recommended reading: four articles written by DNA barcoding educators describing lesson plans, learning objectives, and experiences running their courses. For teachers, these articles might be…

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Bento Lab 🧬

@theBentoLab

7 months

Have you heard about touch-down and step-down #PCR ? Touch-down PCR is a method that automatically "finds" the optimal annealing temperature of your PCR to increase specificity, while also encouraging a high yield. A touch-down PCR program starts with a high annealing…

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Bento Lab 🧬

@theBentoLab

3 months

For anyone learning or teaching bioinformatics, or if you’re interested in getting started, you may like to check out some of many (>230!) integrated tutorials for the Galaxy bioinformatics platform at . The Galaxy platform is a free, easy-to-join,…

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Bento Lab 🧬

@theBentoLab

7 months

For anyone interested in cheap “homemade” DNA extractions using spin columns, or learning what is in most commercial kits, here’s a great modular system of extraction methods called “Mu-DNA”. Mu-DNA stands for “Modular Universal DNA extraction method", and it should be able to…

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Bento Lab 🧬

@theBentoLab

4 months

For anyone wanting to learn more about DNA extraction and eDNA, here's a very useful preprint by @jess_rieder and colleagues that aims to help ecologists, conservation managers, and future eDNA researchers understand how DNA extraction methods work. It's written for readers…

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Bento Lab 🧬

@theBentoLab

6 months

Here’s a recipe for a cheap but effective DNA and RNA preservative solution for preserving animal tissues, their associated microbiomes, and possibly other tissue and DNA sources as well. The solution is known as “Nucleic Acid Preservation” or NAP buffer, and is more fully…

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Bento Lab 🧬

@theBentoLab

7 months

Did you know that you can use modified primers to block PCR for specific unwanted DNA targets? For example, you could block unwanted human DNA in environmental samples, or unwanted host DNA for dietary, parasite, or endosymbiont studies. Blocking primers are oligonucleotides…

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Bento Lab 🧬

@theBentoLab

4 months

For anyone interested in using portable DNA sequencing with Oxford @nanopore MinION as a teaching and capacity-building tool in conservation and biodiversity research, here is a great article by Watsa et al. (2020) that has training advice, case studies, step-by-step protocols,…

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Bento Lab 🧬

@theBentoLab

4 months

Here's a very exciting PCR-enhancing method that might be able to massively improve your PCR yields and sensitivity, while also being suitable for low-resource scenarios: "NanoPCR" using magnesium oxide nanoparticles as a PCR additive while omitting magnesium chloride as a…

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Bento Lab 🧬

@theBentoLab

7 months

Can you use laundry detergents instead of laboratory detergents and enzymes to make an extremely cheap and accessible DNA extraction method with no refrigeration requirements? Here are a few examples of people who have tried this and made laundry detergent extractions a reality:…

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Bento Lab 🧬

@theBentoLab

4 months

Here’s a really interesting example of two articles, 26 years apart, describing how to cut down PCR run time and power usage by ~50% with standard equipment and reagents by optimizing your PCR program and trimming down denaturing and extension times to the bare minimum. This…

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Bento Lab 🧬

@theBentoLab

5 months

Weekend reading 📖 🧬 DNA Extraction Using Microwaves 🧬 Touchdown PCR with Bento Lab Pro 🧬 Rapid Extraction of Very High Molecular Weight Plant DNA

Microwave DNA Extraction & Rapid Extraction of HMW Plant DNA

bento.bio

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Bento Lab 🧬

@theBentoLab

5 months

For anyone looking for freeware electrophoresis gel analysis software, check out GelAnalyzer 23.1 by Dr. Istvan Lazar Jr. and Dr. Istvan Lazar Sr. As you can guess from the version number this software has been around for a while (since 2010) and has been quite popular over this…

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Bento Lab 🧬

@theBentoLab

5 months

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…

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Bento Lab 🧬

@theBentoLab

4 months

Here’s a homemade magnetic nanoparticle DNA extraction method for high-quality genomic DNA. It might save your lab lots of money, sample processing time, or allow you to stop using chloroform if you use CTAB/chloroform extractions. The method, by Wang et al. (2024) was designed…

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Bento Lab 🧬

@theBentoLab

7 months

Here's a simple but ingenious method of doing nested #PCR in a single tube to avoid cross-contamination. Some background: Nested PCR is an extremely sensitive amplification technique using two PCRs in a row, with the second PCR using primers internal to the first set, and DNA…

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Bento Lab 🧬

@theBentoLab

4 months

Here’s a review of DNA extraction methods developed for point-of-need DNA-based testing that could be useful for DNA testing practitioners, students of PCR, fieldwork researchers, and anyone interested in DNA extraction chemistry. The authors, Lee et al. (2023), review methods…

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Bento Lab 🧬

@theBentoLab

5 months

Here’s a cool study that found that direct PCR (putting cells directly into the PCR mix) can be used for DNA barcoding marine and freshwater microalgae from liquid culture, saving a lot of money and time compared to conventional DNA extractions. A key step for some strains is to…

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Bento Lab 🧬

@theBentoLab

3 months

Here’s a very simple and clever method of loading up to 800 μL of a nucleic acid solution into a single well of an electrophoresis gel, allowing the detection, concentration, and recovery of extremely dilute DNA without the need for additional equipment or reagents. The method,…

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Bento Lab 🧬

@theBentoLab

5 months

For anyone needing very high purity high molecular weight genomic DNA (HMW gDNA) for long-read sequencing from complex samples, here is an article describing a new gel electrophoresis purification method that allowed the authors to extract DNA of high purity with a length of >50…

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Bento Lab 🧬

@theBentoLab

6 months

Here is the simplest high-throughput plant DNA extraction method we’ve seen so far, and one that uses the least amount of plastics: just poke a fresh leaf with a 1 to 5 mm piece of fishing line and put the line straight into a PCR! This method, called “Line-PCR” by the authors…

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Bento Lab 🧬

@theBentoLab

6 months

Did you know that microwaving to burst open cells can be a useful method of DNA extraction, especially for cheap, rapid, and high-throughput workflows? It can be used as a step within the extraction process to improve cell lysis, and also as the main cell lysis process to…

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Bento Lab 🧬

@theBentoLab

4 months

Here's a new article validating the quick and super-easy "Squash PCR" method for microalgae cultures, by Yuan et al. (2024). This method could be useful to anyone working with pure cultures or samples of microorganisms that can be easily squashed by hand. It might also be…

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Bento Lab 🧬

@theBentoLab

4 months

If you’re interested in DNA barcoding in a fieldwork or resource-limited context and would like to improve phylogenetic resolution without spending too much money, here’s a method that allows the sequencing of three unlinked regions (COI, CytB, and 18S-ITS-28S) using long…

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Bento Lab 🧬

@theBentoLab

1 month

For anyone wanting to learn or teach basic phylogenetics for DNA barcoding and identification, here are three introductory tutorials for identifying fungi, tardigrades, and flies, all using the free MEGA package for molecular evolutionary genetics analysis. All three tutorials…

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Bento Lab 🧬

@theBentoLab

4 months

For anyone teaching or learning DNA barcoding, here's an article describing three 1.5-hour introductory lesson outlines for high school students, designed as part of a two-week summer school program in Hawai'i. The lessons are focussed around the DNA barcoding of algae but could…

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Bento Lab 🧬

@theBentoLab

6 months

For anyone wanting to make cheap homemade DNA storage cards similar to commercially available FTA cards by Whatman, details of an easy-to-make formulation tested on plants can be found here: Jia et al. (2021). DNA purification-free PCR from plant tissues. Plant and Cell…

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Bento Lab 🧬

@theBentoLab

3 months

Here’s a simple and very inexpensive method of removing PCR inhibitors from samples and crude DNA extracts using low melting point agarose. It’s been used for difficult samples such as soils, feces, human or animal tissues, or phenolic-rich plant tissues. The method, described…

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Bento Lab 🧬

@theBentoLab

3 months

Here’s a DNA extraction method called “HotSOAK” designed for extracting DNA from whole fruit flies and other tiny invertebrates while preserving the morphology for later identification purposes. The method is gentle on specimens, rapid, cost-effective, and suitable for bulk or…

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Bento Lab 🧬

@theBentoLab

27 days

For anyone learning or teaching pipetting, here are four great exercises for accurate pipetting and dilution skills, including one with a glucose monitor (very cool!), a simple dye-based exercise, pipetting incorrectly on purpose, and a friendly classroom “Pipetting Olympics”!…

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Bento Lab 🧬

@theBentoLab

4 months

For aquatic eDNA enthusiasts, here’s an interesting and useful review of the last 10 years in the field by Takahashi et al. (2023), covering 447 articles and including 522 single-species primers and 141 metabarcoding primers. This could be a good article to read if you want:…

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Bento Lab 🧬

@theBentoLab

6 months

Here is a very interesting alkaline DNA extraction method for diverse microorganisms that allows DNA to remain intact in fractured cells, allowing amplification of DNA fragments of up to 6,500 bp (and possibly more?)! The study, by Liu et al. (2022), aimed to find a quick,…

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Bento Lab 🧬

@theBentoLab

3 months

For anyone interested in teaching or learning DNA methods and PCR outreach, here’s a very well-designed two-session practical workshop plan for 17-year-olds, developed by Rouzière & Redman (2011) as an outreach activity for university biology or chemistry departments. The…

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Bento Lab 🧬

@theBentoLab

5 months

Weekend reading 📖 🧬 Free Electrophoresis Gel Analysis Software 🧬 Lab @Home Vlog 🧬 Super-High-Throughput DNA Barcoding with @nanopore MinION

GelAnalyzer 23.1 & Super-High-Throughput MinION DNA barcoding

bento.bio

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Bento Lab 🧬

@theBentoLab

4 months

For anyone wanting cost-effective magnetic bead cleanups for DNA purification or DNA extraction, here’s an easy protocol to turn 15 mL of Sera-Mag magnetic carboxylate beads into 500 mL of “DNA-cleanup-ready” suspension. The protocol, published on by…

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Bento Lab 🧬

@theBentoLab

6 months

Do you want faster PCR for target detection using small amplicons? Here’s a very interesting method for a two-temperature PCR method that cycles sharply between denaturing and annealing temperatures, with no temperature holds, that can cut down conventional PCR run times by at…

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Bento Lab 🧬

@theBentoLab

3 months

For anyone interested in DNA barcoding of plants, or DNA barcoding in general, here is a useful new review of the current state of knowledge by Letsiou et al. (2024). It provides a comprehensive, but not too technical, overview of the progress of plant DNA barcoding, during…

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Bento Lab 🧬

@theBentoLab

8 months

For anyone interested in field DNA sequencing with Bento Lab and Oxford @nanopore MinION, this excellent and extremely detailed review of in-situ sequencing with portable equipment is a very good place to start: Pomerantz et al. (2022). Rapid in situ identification of biological…

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Bento Lab 🧬

@theBentoLab

4 months

Here’s a great one-tube, four-step, 5–15 min DNA extraction method for on-bead PCR using alkaline polyethylene glycol (PEG) and paramagnetic beads. It could be very useful for point-of-need testing or other rapid field research. The method, by Lee et al. (2024), is called ASAP…

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Bento Lab 🧬

@theBentoLab

14 days

For anyone starting DNA barcoding work, primer diagrams or maps can be useful to visualise where primers bind to DNA regions; where they overlap or nest; and to suggest different primers. Here are a few examples, and let us know if you have any better ones! 👇 🐝🐄 🐟 For…

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Bento Lab 🧬

@theBentoLab

3 months

For anyone learning about PCR, or wanting a refresher on what substances can stop your PCRs working, here is a great (if not entirely up to date) review of PCR inhibitors and approaches to resolving PCR inhibition: Schrader et al. (2012). PCR inhibitors–occurrence, properties…

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Bento Lab 🧬

@theBentoLab

7 months

Here's a very useful diagram of recommended DNA barcoding processes, featured in a recent study of the problems in invertebrate DNA barcoding. Has anyone seen a better one? If you have, please let us know! The blue lines indicate a basic DNA barcoding process, while the orange…

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Bento Lab 🧬

@theBentoLab

29 days

Here’s a long-established and very useful method for isolating a single PCR amplicon of interest from an agarose gel called “Band-stab PCR”. In this method, a PCR product is run on an agarose gel, visualised using UV or blue light transillumination, and a visible band from a PCR…

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Bento Lab 🧬

@theBentoLab

13 days

For anyone working with PCR and "recalcitrant" plants full of PCR inhibitors, here are two simple and inexpensive DNA extraction methods that might be useful, using TE buffer, a detergent (SDS), and (unusually!) acetone to remove PCR inhibitors and precipitate DNA! 👇 Both…

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Bento Lab 🧬

@theBentoLab

5 months

For any plant pathologists or fungus enthusiasts doing DNA barcoding, here’s a one-tube rapid DNA extraction method from diseased tissue or tiny immersed fruitbodies that might be useful for DNA-based identification of plant pathogens. The method was developed by Dong et al.…

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Bento Lab 🧬

@theBentoLab

6 months

Here’s a simple, cheap, rapid, and solvent-free DNA extraction method that might be worth trying for plants that contain high levels of PCR inhibitors. It was developed to help detect banana bunchy top virus (a single-stranded DNA virus) in banana leaves. Banana leaves contain…

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Bento Lab 🧬

@theBentoLab

3 months

Here’s a new low-cost method for extracting DNA from biological material from tape lifts, costing an estimated 12p/sample compared to an estimated £3.50/sample for the commercial kit used in the study, while producing comparable results to the kit for saliva and blood. The…

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Bento Lab 🧬

@theBentoLab

6 months

Here is a great application of high-throughput DNA barcoding using Oxford Nanopore MinION: fighting the illegal pangolin product trade by sequencing 2346 scales at a cost of less than 1 USD per sequence! The study, by Yeo et al. (2023), is probably the first study to use…

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Bento Lab 🧬

@theBentoLab

4 months

Here's an article that shows how (semi-) quantitative digital droplet PCR can be done using a homemade microfluidic droplet prototyping toolkit. The authors detected and roughly quantified human GAPDH RNA transcripts using standard PCR laboratory equipment - very cool! By way of…

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Bento Lab 🧬

@theBentoLab

3 months

For anyone looking for a cheap and quick method for drying DNA for short-term to medium-term storage or shipment of DNA extracts, here’s a very interesting article testing the protective effects of drying DNA with Tris-buffered polyvinyl alcohol or trehalose. In this article,…

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Bento Lab 🧬

@theBentoLab

1 month

How small a PCR volume can you use for PCR and metabarcoding to save reagents and money, and does it have any effect on the results? Here’s an encouraging article from Buchner et al. (2021) that found no significant differences in metabarcoding results using PCRs of 5 µl to 50…

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Bento Lab 🧬

@theBentoLab

2 months

For anyone interested in DNA metabarcoding arthropods, here’s a great article on the validation of commonly used and newly developed COI metabarcoding primers, testing 36 primer sets on a) a mock community containing 374 insect species, and b) a malaise trap sample. The authors…

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Bento Lab 🧬

@theBentoLab

6 months

Here’s a recently published workflow for high-quality @nanopore metagenomic sequencing using Bento Lab and other portable equipment, for use outside the laboratory, taking less than three hrs for DNA extraction and library preparation. The authors (Bloemen et al., 2023)…

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Bento Lab 🧬

@theBentoLab

6 months

Weekend reading on #PCR 📖 🧬 Cheap DNA Extractions Using Laundry Detergents 🧬 HotSHOT DNA Extraction Kit 🧬 Papers We Love: BaseLess — DNA detection using #MinION without basecalling

Laundry Detergent DNA Extractions & DNA detection using MinION without basecalling

bento.bio

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Bento Lab 🧬

@theBentoLab

1 month

In the quest for faster and more portable diagnostic PCRs, here is a new qPCR method called “FlashPCR” by Bustin et al. (2024) that allows a 10-15 min PCR on standard qPCR cyclers. It could save valuable time in point-of-care medical testing, and importantly could help make…

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Bento Lab 🧬

@theBentoLab

28 days

Here’s an ingenious PCR method called COLD-PCR, designed for the preferential enrichment of low-abundance DNA sequence variants even when the variant is unknown. It was first described in 2008 and has since been used intensively in cancer diagnostics and other medical research.…

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Bento Lab 🧬

@theBentoLab

18 days

Here’s a free downloadable costing & budgeting spreadsheet tool to help you fully cost your PCR lab work; calculate what you need to buy (and how much); or to help you plan what to take on fieldwork. Great for PCR beginners, and hopefully useful for the more experienced too! 👇…

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Bento Lab 🧬

@theBentoLab

2 months

If you want to do country-wide citizen science while training up high school students in eDNA and qPCR, here is one way to do it: an inspiring example of “extreme citizen science” by the Natural History Museum of Denmark between 2022-2023 via the DNA & Life project. This…

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Bento Lab 🧬

@theBentoLab

7 months

Sunday reading 📖 🧬 A guide to @nanopore #MinION #DNAbarcoding in the field 🧬 PCR and Education: assays to detect onion colour and rice fragrance 🧬 Dipstick DNA Extraction Kits back in stock

DNA Dipsticks and a MinION Field Barcoding Guide

DNA Dipsticks, a MinION Field Barcoding Guide, and Two PCR Assays for Education and Learning

bento.bio

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Bento Lab 🧬

@theBentoLab

4 months

For anyone interested in PCR in education, here’s a useful article describing an introductory undergraduate module based around PCR and sequencing of genes for the detection of heritable human traits. The article, by Shanle & Trubitsyn (2020), could be useful for teachers or…

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Bento Lab 🧬

@theBentoLab

1 month

For anyone looking for a simple PCR experiment for high school or secondary school students, here’s a great lab practical looking at length variations in a highly variable region of chloroplast DNA across different plant species. It could be used as a stand-alone lesson to learn…

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Bento Lab 🧬

@theBentoLab

2 months

For any insect DNA barcoders, here's a rapid and inexpensive high-throughput microwave DNA extraction method for soft-bodied insects such as flies, that aims to cause minimal or no damage to the specimen morphology while releasing enough DNA for PCR. The method, by Stein et al.…

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Bento Lab 🧬

@theBentoLab

2 months

For anyone looking for a simple, rapid, non-toxic genomic DNA extraction method, here’s a classic method that has over 3760 citations and is still widely used today. It was originally designed for plants but has occasionally been used for animal or fungal DNA, and has many…

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Bento Lab 🧬

@theBentoLab

1 month

If you’re interested in rapid in-situ metagenomics with Oxford @nanopore MinION, here’s a great example of how a lab-in-a-suitcase approach can achieve same-day on-site results, allowing “real-time functional and taxonomic monitoring of microbial communities in remote areas”.…

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Bento Lab 🧬

@theBentoLab

8 months

If you’re interested in high-throughput DNA barcoding using Oxford @nanopore MinION, but you've never tried any bioinformatics workflows, you might like to learn about ONTbarcoder. It's a great piece of software for DNA barcodes that are protein-coding genes like COI, which are…

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Bento Lab 🧬

@theBentoLab

6 months

For anyone interested in extracting very high molecular weight plant genomic DNA, here is a rapid, simple and economical method suitable for single molecule sequencing. The method essentially gently lyses cells in a novel extraction buffer to release intact nuclei which are…

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Bento Lab 🧬

@theBentoLab

3 months

Here’s a very nice detergent-based variant of the hot alkaline lysis DNA extraction method with additives for the PCR to remove PCR inhibitors. It was designed for high-throughput genotyping of plants (including potentially PCR-inhibiting samples), but it's also been used for…

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Bento Lab 🧬

@theBentoLab

8 months

If your PCR isn’t working, one quick and easy thing to try is diluting the DNA extract and seeing if that helps. It’s often counter-intuitive, but PCR only needs an extremely small number of molecules of template DNA present to amplify successfully (much less than are usually…

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Bento Lab 🧬

@theBentoLab

3 months

For anyone interested in metabarcoding mosquitos for vector and pathogen surveillance, here’s a recent study (possibly the first) demonstrating the use of @nanopore technologies and DNA metabarcoding for surveying mosquito vectors in bulk samples. A few nice snippets: 🦟Using…

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Bento Lab 🧬

@theBentoLab

7 months

Here’s an article about a very exciting technique for field DNA analysis: direct detection of target DNA from raw Oxford Nanopore MinION signals using trainable neural networks, running without basecalling on a $100 single-board computer. A group of researchers aiming to achieve…

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Bento Lab 🧬

@theBentoLab

6 months

Do you share and maintain your preferred lab protocols publicly, outside of a methods section? We saw a neat small collection of mycology protocols on Github from @CamilleTruong3 (thanks @MYCOmmunityAM ) What else do people use? 🔗

Welcome!

All things fungi

camillethuyentruong.github.io

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Bento Lab 🧬

@theBentoLab

4 months

For anyone interested in soil eDNA, here’s a great article that tested and recommends a simple silica gel drying method for preserving soil samples and associated bacterial and fungal DNA for up to three weeks. The method is easy-to-use and cost-effective, so it could be…

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Bento Lab 🧬

@theBentoLab

5 months

Method tip: Need a quick DNA extraction solution? The alkaline PEG-200 reagent is an ingenious one-tube, direct to PCR, DNA extraction method by Chomczynski & Rymaszewski (2006). The solution is easy-to-make: it combines PEG-200, KOH, and water, and creates a high pH…

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Bento Lab 🧬

@theBentoLab

3 months

For anyone interested in mobile diagnostics in resource limited scenarios, here’s a very exciting feasibility study of portable sequencing using @nanopore MinION and Bento Lab for genomic surveillance of malaria, by @AurelHolzschuh et al. (2024) (article link below 👇). Malaria…

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Bento Lab 🧬

@theBentoLab

2 months

Here’s a very cheap, rapid, accessible, and scalable DNA purification method suitable for viral RNA or bacterial DNA. It's been validated for use in SARS-CoV-2 (COVID-19) detection, and has more recently been used to purify DNA to allow the detection of toxin-producing E. coli in…

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Bento Lab 🧬

@theBentoLab

5 months

Here’s an idea for a perfect festive gift for any PCR lab anywhere: a cheap salad spinner centrifuge for PCR strips, plates, or any tube you can make a fitting for. They’re effective, cheap to buy, easy to modify, lightweight, and portable — a gift that will be appreciated with…

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Bento Lab 🧬

@theBentoLab

4 months

For anyone looking for a more advanced application of DNA sequencing in education, here’s one inspirational example: the generation of gastropod mitochondrial genomes using Oxford Nanopore sequencing as part of a biodiversity curriculum for graduate students. This study, by a…

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Bento Lab 🧬

@theBentoLab

12 days

Here’s an interesting alkaline lysis DNA extraction method in which ammonium sulphate is used as a neutralising agent rather than Tris-HCl buffer. It allows the amplification of low-copy and larger genes from fungal cultures, and could be useful for other applications too👇 The…

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Bento Lab 🧬

@theBentoLab

7 months

Here's a very cool video that shows how you can survey rare mammals, birds, and reptiles by metabarcoding DNA picked up by roadside flies using @nanopore or Illumina sequencing! You can read more about how it was done here: Srivathsan et al. (2022). Network analysis with…

Amrita Srivathsan

@asrivath

2 years

iDNA from roadside flies detects rare mammals, birds, and reptiles. New and simple protocol: dissolve fly poop in water, metabarcode with MinION or Illumina. >400 flies belonging to 25 species ==> 294 identifications ==> 20 vertebrate species. @nanopore

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Bento Lab 🧬

@theBentoLab

2 months

For anyone DNA barcoding or genotyping plants, here is an interesting direct PCR method that uses inexpensive alkaline pH buffers for grinding, heating, and protein denaturing, resulting in crude but PCR-amplifiable DNA extracts. The authors successfully used it for plants from…

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Bento Lab 🧬

@theBentoLab

1 month

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…

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Bento Lab 🧬

@theBentoLab

8 years

The world’s first accessible DNA lab, #BentoLab is now on Kickstarter! Bento Lab = Biology for Everybody

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Bento Lab 🧬

@theBentoLab

1 month

Here’s one way to increase the concentration of limited very low concentration DNA in a PCR: dry up to 10 μL of DNA extract in the bottom of a PCR tube, and then do a reduced volume PCR of 15 μL to 5 uL. This method comes from Gaines et al. (2002), who investigated the role of…

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Bento Lab 🧬

@theBentoLab

5 months

📖 Top 10 Holiday Reading Tips, including... 🧬 Direct PCR for microalgae 🧬 Blocking Primers 🧬 Single-tube nested PCR 🧬 Mu-DNA - modular DNA extraction system

Festive Greetings & Top 10 Articles We’ve Shared in 2023

Festive Greetings & Top 10 Articles & Methods We’ve Shared in 2023

bento.bio

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Bento Lab 🧬

@theBentoLab

2 months

Here’s a lovely clear definition and explanation of “step-up PCR”, a procedure used to improve PCR when primers may have some mismatches to the target DNA. It’s from the earliest reference I can find so far for this method (Palumbi, 1996), but it may well have been developed…

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Bento Lab 🧬

@theBentoLab

25 days

For anyone working with animal dung and DNA, here's a new study that found storage in Longmire’s Lysis Buffer was superior to ethanol for @nanopore MinION metabarcoding, for diverse animals such as cows, bears, tapirs, and monkeys, for up to 20 days at room-temperature and 461…

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Bento Lab 🧬

@theBentoLab

7 months

For anyone considering designing their own target-specific primers, one great tool you should know about is Primer-BLAST. Primer-BLAST is a very popular and highly cited web-tool created at NCBI () to help people design primers and check for specificity…

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Bento Lab 🧬

@theBentoLab

19 days

Today is #WorldDNADay , commemorating the discovery of the structure of DNA in 1953 & completion of the Human Genome Project in April 2003. It's also a good day to celebrate PCR, so here's an easy-reading history of the polymerase chain reaction plus a few landmark articles 👇…

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Bento Lab 🧬

@theBentoLab

7 months

📖 Sunday reading for PCR enthusiasts: 🧬 Modular Universal DNA Extraction method using homemade extraction buffers 🧬BarKeeper, free DNA barcode analysis 🧬 Problems in DNA barcoding practices and suggested solutions

MuDNA, BarKeeper, and Problems with DNA Barcoding Workflows

bento.bio

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Bento Lab 🧬

@theBentoLab

3 months

For anyone interested in plants and DNA barcoding or genotyping, here's an article from 2013 showing that stabbing leaves of woody plants with a toothpick multiple times, and dipping the toothpick in a PCR mix or TE buffer, can produce enough amplifiable DNA for direct PCR. The…

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Bento Lab 🧬

@theBentoLab

7 months

Sunday reading 📚 🧬 A primer on pollen #metabarcoding using @nanopore MinION 🧬 Methods and Techniques: Booster #PCR + Touchdown and Stepdown PCR

Pollen ID using MinION, Booster PCR and Touchdown PCR

Pollen ID using MinION, Booster PCR, and Touchdown and Stepdown PCR

bento.bio

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Bento Lab 🧬

@theBentoLab

8 months

Here’s a super-easy method of DNA extraction that could be tried for DNA barcoding a wide range of invertebrate species : Just place a small tissue sample in phosphate-buffered saline (PBS), squash if soft-bodied, heat for 2 min at 98 C, and use some of the solution directly for…

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Bento Lab 🧬

@theBentoLab

11 days

Here’s a super-useful tip from @idtdna (Integrated DNA Technologies) that allows you to use primer sequences & NCBI’s BLAST search to calculate the expected length of an amplicon, provided there are appropriate matches in reference databases that include the primer sequences 👇…

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Bento Lab 🧬

@theBentoLab

22 days

For anyone interested in communities of cryptograms (e.g. of lichens, non-lichenised fungi, bryophytes, microalgae, biocrusts, or biofilms), here's a great direct PCR DNA barcoding approach that allows the simultaneous processing of 4 different taxonomic groups in ~1 hr 6 mins!…

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Bento Lab 🧬

@theBentoLab

6 months

For anyone interested in simple eDNA work for beginners or use in low-budget scenarios, here's an eDNA detection strategy called GoFish that can be done with basic laboratory equipment. The authors, Stoeckle et al. (2018), developed GoFish for situations where fish eDNA targets…

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Bento Lab 🧬

@theBentoLab

1 year

Researchers from Peru have developed a low cost molecular toolkit for COVID-19 detection using open-source locally produced reagents. To test portable applications they showed proof of concept by running workflows with Bento Lab. 👇🧵[1/6]

An open-source toolkit for Covid detection

Mass PCR-testing has been a key component of the response to the SARS-COV-2 (COVID-19) pandemic to inform quarantine measures and infection rates. However, this relies on having the capacity to test…

bento.bio

1

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Bento Lab 🧬

@theBentoLab

8 months

Awesome to see Bento Lab being used in a suitcase/backpack eDNA laboratory alongside @nanopore MinION as part of the West African Marine Fish DNA Barcoding Network (WAMBA NET)! 🐟🧬 You can find out more about the exciting and important work that this project is doing here:…

Ouattara Koffi Nouho

@OuattaraKoffiN1

8 months

“Setting up a suitcase eDNA Laboratory/Lab in backpack for barcoding : MinION sequencing”. Wonderful week sharing my experience with WAMBA NET (West African Marine Fish DNA Barcoding Network) participants from Cameroon; CI ; Ghana ; Mauritania ; Nigeria ; Sénégal and France.

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Bento Lab 🧬

@theBentoLab

5 months

Here’s a great in-depth investigation into how best to release DNA from cotton swabs, resulting in a homemade low-cost rapid DNA extraction method for direct PCR with up to 60–80% recovery of input DNA (depending on sample type). The article, by Gray et al. (2023), addresses the…

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Bento Lab 🧬

@theBentoLab

3 months

Here’s a new technical report on DNA extraction methods from the European Network of GMO Laboratories. It's written for analytical lab personnel, but it could also be useful for anyone extracting DNA from animals or plants, or for students interested in the bioscience industry.…

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