Daniela Miller

I did it! I earned my doctorate degree. And with some time to sink in, it finally feels real. 🎓 To do it by bringing my vision of whole-genome assembly in wheat to life made it truly a dream come true. 🥰

Need to collect wheat roots & other tissues for RNA-seq or Iso-seq experiments? Here's a method that uses controlled conditions in a growth chamber to minimize sample contamination. 🌱 protocols.io/view/hydroponi…

Weihnachtsmarkt in Wuppertal, DE ☃️

Happy Halloween! 🎃👻 May your cold & flu season be #biohazard free. 😷

@SigmaFacto Gotta love those Midwest US crop monuments 😂

Drove by a corn field Monday morning. I wonder how many TEs in them to be able to grow so big in mid March Ohio?

@theBentoLab Awesome! I find magnetic beads are great to work with once you get used to them. How do the fragment lengths compare with CTAB?

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 for genomic DNA extraction from crop plants. It aimed to replace the chloroform phase separation step in traditional CTAB/chloroform extractions with a paramagnetic bead step using homemade salicylic acid-coated magnetic beads. The authors claim: ⭐ It’s capable of isolating high-quality genomic DNA from leaf tissue and seeds in less than 2 hours ⭐ It uses fewer steps than a standard CTAB extraction method ⭐ The cost of the nanoparticles is $7.31 a gram, and only 120 ng is used per sample! So substantially cheaper than commercially available magnetic beads. Synthesis of the nanoparticles also looks relatively straightforward for anyone with some basic chemistry experience, a magnetic stirrer and hotplate, and some nitrogen gas. It should be possible to do the synthesis in a home lab with a bit of ingenuity (doing it under nitrogen may be a bit difficult), but if you belong to a university and have a nearby chemistry department then they would probably find it easy to produce the nanoparticles. The protocols are also available here: protocols.io/view/crop-dna-… Here’s the article: Wang, H., Zhao, X., Tan, L., Zhu, J., & Hyten, D. (2024). Crop DNA extraction with lab-made magnetic nanoparticles. Plos one, 19(1), e0296847. #pone.0296847.ref011" target="_blank" rel="nofollow noopener">journals.plos.org/plosone/articl… The original methods to produce the magnetic nanoparticles (slightly different to the above article) , and to use them for DNA extraction, can be found here: Unal et al. (2010). Synthesis, conductivity and dielectric characterization of salicylic acid–Fe3O4 nanocomposite. Materials Chemistry and Physics, 123(1), 184-190. researchgate.net/publication/24… And here: Zhou et al. (2013). One-stop genomic DNA extraction by salicylic acid-coated magnetic nanoparticles. Analytical biochemistry, 442(2), 249-252. ncbi.nlm.nih.gov/pmc/articles/P…

@MaizeZynskiHI Yep, there's nothing like finding a gem in someone's 1970s PhD dissertation. 😯

Yes!!! Preach!!! "At the same time, we remind young scientists that sometimes the answers to our questions can be found in the old literature, often neglected in the modern era of scientific research." cell.com/trends/plant-s…

CryoEM structure of an intrinsically disordered protein

@wheatgenome Congratulations, Carolyn! 👏🎉🧬

Congratulation Carolyn Mukiri Kambona for your #IWGSC-Feuillet Early Career Award Wishing you a great career in wheat research!

Happy holidays!

A delightful thread, but this one is my favorite for both the quality of infographics and fashions.

Today, we launch 1st of a series of Fellowships in Biodiversity Genomics & Bioinformatics for African scientists: The African Genome Center -  @DAISEA_AfricaBP Open Institute Joint Fellowship in Biodiversity Genomics & Bioinformatics 2024. Click to apply: tinyurl.com/africabp-fello…

Big Congratulations to Carolyn Mukiri!! 👏👏👏

@ThompsonPeerLab @UCIBioSci @UCIrvine It's wild how those little walls will create more bench space 🤯 what a lovely lab!

More photos of our beautiful new lab space. @UCIBioSci @UCIrvine

This is a lake today at Badwater in Death Valley National Park, from all the runoff during huge rains from #HurricaneHillary remnants in August. The salty lake is slowly evaporating.

Trying to study genes while refusing to study the genome around them will never make sense to me. Be the curious chickadee you wish to see in the science world! 🐣

"Generative culture is one oriented on performance, where potentially damaging information is welcomed and distributed to the right people to act on." Contrasted to pathological & bureaucratic cultures. A worthwhile quick read on research integrity, safety culture, and trust.

Now that's what I call a crop rotation💞

Some impressive genomic heavy-lifting here! Congratulations to all involved! @darwintreelife

@DPortik @jewilki Wow thank you so much for this! A big help. I plan to give it a shot next week. 💪🧬 Will be in touch!

@subgenomes @jewilki Sounds awesome! There are two approaches you can use here. After assembly, run all contigs through the HiFi-MAG-Pipeline. It will tell you if you have bacteria/archaea, and if it is worth it to try an advanced approach. 1/3

@DPortik @jewilki I'm considering using your HiFi-MAG- Pipeline to assemble host-associated metagenomes. Very cool! I'm curious if it can also be used for detection of potential contaminant sequences in host contig assemblies? #hifi #metagenomics