Happy to announce that Ilya Shabanov’s paper – “HARLEY mitigates user bias and facilitates efficient quantification and co-localization analyses of foci in yeast fluorescence images” has been published in Scientific reports. Link here.
This work has two main components. The first is a description of how much variability there is in quantifying yeast stress granules, both between users and even by the same user scoring the same dataset. The second part of the paper is the development and description of software (HARLEY) to accurately and reproducibly quantify yeast stress granules (and other foci) aided by a user-trained model. We also developed an array of useful co-localization tools and outputs. HARLEY runs in the chrome browser and is quite easy and intuitive to learn – you can download it freely, and access various training datasets and documents here – https://github.com/lnilya/harley
Congratulations Ilya on a job well done! We miss you and wish you well in your PhD in North Carolina.
We’re happy to announce that our R01 grant “Analysis of mRNP granule clearance, vacuolar RNA decay and TDP-43 turnover” was renewed by NIGMS for 4 years.
In addition, in collaboration with Dr Sami Barmada (University of Michigan), we have received a 1-year R56 Bridge Funding award from NINDS for our grant “Spatiotemporal analysis of TDP-43 toxicity and endolysosomal turnover mechanisms”.
We are extremely grateful for this support from NIH and hope this leads to various interesting publications from our labs in the coming years.
We are happy to have been part of an interesting study led by the Kraft laboratory (U of A) on the role of Edc3 phosphorylation in P-body dynamics and the pathology of prostate and lung cancer. This is also the first description of our mRNP granule purification method, which we hope to share in more detail in the near future.
We also contributed to an extensive resource (Guidelines for the use and interpretation of assays for monitoring autophagy) lead by Dan Klionsky, which is an invaluable resource in the field.
Nikita has published a 1st author paper in the journal Biomolecules, concerning the role of SGs in TDP-43 phenotypes, using yeast and human cell studies. Congrats Nikita! Thanks to our collaborators also (Ivanov and Bolger labs).
Hearty congratulations to Nikita Fernandes who graduated in August 2020 (with two first author research manuscripts, a co-authorship and two first author reviews to her name). Not too shabby! We look forward to seeing what the future brings for you!
Very happy to announce a first author paper for Nikita in the journal Nucleic Acids Research. We describe an interesting new mechanism by which P-bodies in yeast are scaffolded by an mRNA 3’UTR via a “cis-translation” dependent mechanism. Congrats Nikita!
Yay! A co-first author paper in Molecular and Cellular Biology for Guangbo and Aaron, with significant contributions from Amanda, Fen, Eman and Allison also. A follow up to our work on the role of endocytosis in turnover of aggregation-prone RNA binding proteins implicated in ALS pathology. Well done folks!
Nichole, in collaboration with the Capaldi lab, has published a letter in the journal RNA detailing various methods for assessing mRNA decay, and their effects on stress signaling pathways. Nice job guys!
A momentous day in the lab – our first grad student, Nichole, successfully defended her Ph.D on the regulation of cytoplasmic mRNA decay. More pictures to follow but for now, suffice to say – we’re all very proud of you Nichole, and look forward to seeing what the future brings!
