Small regulatory RNAs (sRNAs) are thought to function in trans-species regulation between host and parasite/pathogen. Our work examined this system in parasitism by the noxious weed Cuscuta campestris, finding numerous micro RNAs (miRNAs) which regulate host mRNAs. Recent work has looked broadly at the Cuscuta genus, finding that the parasite produces a broad spectrum of sRNAs which can target host mRNAs. Furthermore, this provides an evolutionary paradigm by which the parasite can maintain targeting in-spite of host adaptation.
NR Johnson, CW dePamphilis, and MJ Axtell. Compensatory sequence variation between trans-species small RNAs and their target sites, BioRxiv (2019) - Preprint
NR Johnson, and MJ Axtell. Small RNA warfare: exploring origins and function of trans-species microRNAs from the parasitic plant Cuscuta, Curr. Opin. Plant Biology (2019) - Review
S Shahid, G Kim, NR Johnson, E Wafula, F Wang, C Coruh, V Bernal-Galeano, T Phifer, CW dePamphilis, JH Westwood, and MJ Axtell. “MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs”. Nature (2018) - Research
Alignment and annotation of sRNA-seq data suffers from high-rates of ambiguously mapping reads. Methods in the field inadequately solved this problem, leading us to implement algorithms for estimating read alignment in our lab’s tool: ShortStack. Testing against simulated and real data show that this new method in ShortStack is much more precise in aligning miRNAs and small interfering RNAs than other available methods.
A Lunardon, NR Johnson, E Hagerot, T Phifer, S Polydore, C Coruh, and MJ Axtell. Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants. BioRxiv (2019) – Preprint
NR Johnson, J Yeoh, C Coruh and MJ Axtell. Improved Placement of Multi-Mapping Small RNAs. G3 (2016) - Research
Xylan is one of the most common polymers in the essential cell wall component: hemicellulose, but the molecular machinery directly responsible for its synthesis was unclear. This project detailed phylogenetic analysis of gene families to narrow a search for this protein. Protein expression in N. benthamiana and P. pastoris, followed by purification and in vitro as well as in vivo assays helped to discover the enzyme essential for xylan backbone synthesis.
JK Jensen, NR Johnson and CG Wilkerson. “Arabidopsis thaliana IRX10 and two related proteins from psyllium and Physcomitrella patens are xylan xylosyltransferases”. The Plant Journal (2014) - Research
JK Jensen, NR Johnson and CG Wilkerson. “Discovery of diversity in xylan biosynthetic genes by transcriptional profiling of a heteroxylan containing mucilaginous tissue”. Front. Plant Sci. (2013) - Research
This is a collection of silly diversions, some finished and others incomplete. Links are updated at my leisure, meaning that most are missing…
https://github.com/MikeAxtell
Mike Axtell’s github page, where you can find ShortStack and other useful scripts.
http://axtelldata.bio.psu.edu/data/old_scripts/find_3p_adapter/
Box folder containing a perennially useful script: find_3p_adapter.pl. This script can look for a user-supplied common miRNA in untrimmed sRNA-sequencing data to infer what the 3p adapter is. Unbeliveably helpful for when working with publicly available datasets.
https://www.ascb.org/careers/how-to-print-a-fabric-poster/
A guide to printing fabric posters for conferences. The company www.spoonflower.com is the actual service and they do good work. Recently they replaced the “performance knit” with “performance pique” - not as crisp but still a nice poster.