Lightnews — Scholar-powered news

Reposted by Reindert Nijland

Chris Seymour @iiseymour.bsky.social · May 21

Dorado is 1.0! 🎉

LC25 release adds v5.2 DNA/RNA models with a new suite of mod models that are higher accuracy, lower FP rates, and significantly faster.

- Introducing dorado variant 👀
- HAC error rate is down over 25%.
- New 2’Ome mod models
- Hopper & Blackwell SUP speed ups

#Nanoporeconf

8 18

Reposted by Reindert Nijland

Gerome Breen @psychgenomics.bsky.social · May 21

Now clear how much extra information from @nanoporetech.com data - especially full transcripts #nanoporeconf

1 3 2

Reposted by Reindert Nijland

Oxford Nanopore @nanoporetech.com · May 21

At London Calling, Rosemary Sinclair Dokos and Lakmal Jayasinghe shared how we’re doubling down on what matters: delivering a future-ready platform with proven performance across DNA, RNA, and now proteins. Click here to discover what’s new – and why it matters: nanoporetech.com/news/london-...

6 5

Reposted by Reindert Nijland

Auriel Sumner-Hempel @aurielesumner.bsky.social · May 15

Our previously published paper was picked up in local Dutch news as well as here, very exciting to see the media take notice of this work 🦈
@reindertn.bsky.social @w-u-r.bsky.social
#eDNA #Sharks #Rays #OWFs

oceanographicmagazine.com/news/are-off....

Are offshore wind farms the next safe spaces for sharks and rays? - Oceanographic

New eDNA evidence has confirmed the presence of active shark and rays around Dutch offshore wind farms, posing an exciting new question.

oceanographicmagazine.com

2 4

Reindert Nijland @reindertn.bsky.social · Apr 10

Two papers I contributed to, published online on the same day! Both on large charismatic fish from the North Sea: Sharks and Sturgeons! 🦈🦈
Sharks and rays: www.sciencedirect.com/science/arti...
Sturgeons: link.springer.com/article/10.1...

Two young European sturgeons in a white bucket, about to be re-introduced in the wild

2

Reindert Nijland @reindertn.bsky.social · Apr 10

Just out: Our paper on the historical occurrence of sea sturgeons (Acipenser sturio and A. oxyrinchus) in European waters, and consequences for reintroduction!
link.springer.com/article/10.1...

Towards an optimised strategy for reintroducing sea sturgeons (Acipenser sturio and A. oxyrinchus) to Europe - Biodiversity and Conservation

The aim of this paper is to identify an optimised strategy for the reintroduction of two anadromous sturgeon species to Europe: the critically endangered European sturgeon (Acipenser sturio) and the v...

link.springer.com

1

Reposted by Reindert Nijland

Auriel Sumner-Hempel @aurielesumner.bsky.social · Apr 10

📣Excited to share that our new #paper is out! Using #eDNA #metabarcoding to detect #elasmobranchs in #OWFs in the North Sea🦈🦈
www.sciencedirect.com/science/arti...
@reindertn.bsky.social
@nanoporetech.com

6 9

Reposted by Reindert Nijland

Dr.Kat Stewart @ecoevoedna.bsky.social · Mar 20

Great windfarm - elasmobrach #eDNA research by Auriel Summer-Hempel @reindertn.bsky.social @aquaecomics.mastodon.social.ap.brid.gy

1 3 8

Reindert Nijland @reindertn.bsky.social · Feb 11

The reviewer identified a mismatch in the last nucleotide of the 3` side of the forward primer targeting the 12S region, for several species in the order of Gadiformes. The details of that error and its correction are now presented in the supplemental data: onlinelibrary.wiley.com/action/downl...

onlinelibrary.wiley.com

Reindert Nijland @reindertn.bsky.social · Feb 11

Getting this published was a long process, and taught us a lot. We initially made an error in the primer design of our new 2kb 12S-16S amplicon. This was fortunately identified by a added new reviewer in the third review round. So all experiments had to be repeated with updated, correct primers...

1

Reindert Nijland @reindertn.bsky.social · Feb 11

Super happy our paper on #eDNA #metabarcoding of North Sea fish using @nanoporetech.com sequencing is finally published in Molecular Ecology Resources: onlinelibrary.wiley.com/doi/10.1111/...

The Long and the Short of It: Nanopore‐Based eDNA Metabarcoding of Marine Vertebrates Works; Sensitivity and Species‐Level Assignment Depend on Amplicon Lengths

To monitor the effect of nature restoration projects in North Sea ecosystems, accurate and intensive biodiversity assessments are vital. DNA-based techniques and especially environmental (e)DNA metab....

onlinelibrary.wiley.com

1 8 16

Reposted by Reindert Nijland

Chris Kent @chris.primalscheme.com · Dec 23

Fancy some light Christmas reading? I’m happy to share our new preprint, covering the impact and cutting edge improvements to PrimalScheme!

Preprint: www.biorxiv.org/content/10.1...

PrimalScheme: open-source community resources for low-cost viral genome sequencing

Viral genome sequencing using the ARTIC protocol has been a vital tool for understanding the spread of epidemics including Ebola, Zika, COVID-19 and Mpox and has seen widespread adoption due to its lo...

www.biorxiv.org

1 7 15

Reindert Nijland @reindertn.bsky.social · Dec 22

Ik zag laatst op Planken Wambuis dit donkere dier. Maar die had meer de grootte van de reebok wat het samen mee stond te grazen...

1

Reposted by Reindert Nijland

Cameron Thrash @jcamthrash.bsky.social · Dec 12

Bacterial clustering amplifies the reshaping of eutrophic plumes around marine particles: A hybrid data-driven model journals.plos.org/ploscompbiol... #jcampubs

Bacterial clustering amplifies the reshaping of eutrophic plumes around marine particles: A hybrid data-driven model

Author summary Recent lines of evidence highlight the pronounced impact of slow-moving particles on the oceanic carbon cycle and associated ecosystem functions (e.g., CO2 removal, oxygenation, acidifi...

journals.plos.org

4 8

Reindert Nijland @reindertn.bsky.social · Dec 3

I sequenced total genomic DNA on a previously used flow cell. I got about 2x coverage of the whole genome and >100 fold for the mitogenome.

2

Reindert Nijland @reindertn.bsky.social · Dec 3

I sequenced and assembled the full mitochondrial DNA of the angular crab (Goneplax rhomboides) using the @nanoporetech.com #MinION #Mk1D, so #nanopore only. The raw read quality really is amazing, and the assembly looks perfect!
www.ncbi.nlm.nih.gov/nuccore/PQ64...

Alignment of raw nanopore read to create a consensus seqeunce, showing very litte errors in the raw read data

Annotated overview of the mitogenome assembly from Goneplax rhomboides

1 2 16

Reposted by Reindert Nijland

Nathalie Steins @nathaliesteins.bsky.social · Dec 3

Made starter pack of marine scientists working @w-u-r.bsky.social. Anyone missing? Let me know.
@jimvanbelzen.bsky.social @martinbaptist.bsky.social @annetpauwelussen.bsky.social @reindertn.bsky.social @rolfgroeneveld.bsky.social @hansverdaat.bsky.social @evertdefroe.bsky.social
go.bsky.app/Nz4Qtjx

2 7

Reindert Nijland @reindertn.bsky.social · Nov 30

My baby Small-spotted catsharks are still happy, and so much fun to watch!

2

Reindert Nijland @reindertn.bsky.social · Nov 21

These are juvenile small-spotted catshark (Scyliorhinus canicula) hatched in August this year. So cool!

Reindert Nijland @reindertn.bsky.social · Nov 21

Today I got some new guests in my home aquarium! #babyshark #doo-doo-doo

1 1

Reposted by Reindert Nijland

Lachlan Fetterplace @fiskeforbrains.bsky.social · Nov 21

The Marine & Freshwater Research Institute in Iceland seeks a PhD student (funded 4 yr position) to research bycatch of #marinemammals & #seabirds in Icelandic fisheries (with some cross over with us here at SLU on EU projects on bycatch of sensitive species). 🐟🧪🦑🌎

www.hafogvatn.is/en/about/new...

We are seeking a PhD student in marine biology

The Marine and Freshwater Research Institute (MFRI) in Iceland is seeking a PhD student in Marine Biology for a funded full-time position for 4 years with

www.hafogvatn.is

1 51 52

Reindert Nijland @reindertn.bsky.social · Nov 19

I contributed to this article in Pioneering Tech Magazine by TU Delft on the Ecological Impact of offshore wind in the North Sea, including North Sea underwater pictures: www.tudelft.nl/en/innovatio...

Offshore wind: how to balance growth and nature?

As you depart from Schiphol and look out over the North Sea, you’ll see 'islands' of slender, white wind turbines looming below. It’s a serene, futuristic landscape that stands in stark contrast to th...

www.tudelft.nl

1

Reindert Nijland @reindertn.bsky.social · Apr 27

Out now: Review and update on the spread of lionfish in the Mediterranean, led by WUR PhD student @BottaciniD neobiota.pensoft.net/article/1104...

Lionfish (Pterois miles) in the Mediterranean Sea: a review of the available knowledge with an update on the invasion front

Invasive species often severely impact ecosystems and human activities in the areas that they invade. The lionfishes Pterois miles and P. volitans are regarded as the most successful invasive fishes i...

neobiota.pensoft.net

1

Reindert Nijland @reindertn.bsky.social · Apr 4

At Marine Animal Ecology (WUR) we are developing a Biodiversity Sensing box, which combines imaging (both fish and microscopic plankton), acoustics and environmental DNA (eDNA) for marine biodiversity monitoring. More information in the article below

Automatic sampling underwater - Resource online

Measuring biodiversity without divers.

www.resource-online.nl

4

Reindert Nijland @reindertn.bsky.social · Jan 22

We recently published a forum article in Trends in Ecology & Evolution on "Edge computing in wildlife behavior and ecology". One of the presented cases is our biodiversity/fish sensing box:
doi.org/10.1016/j.tr...