Prachee is the co-founder and CSO of Arcadia Science. She comes from the Geisel School of Medicine at Dartmouth where she is an Associate Professor of Biochemistry and Cell Biology. Prachee is also the President of ASAPbio.
Building on the open-source platform PubPub, we’re sharing the first iteration of our publishing website. In addition to posting our first set of research pubs, we’re documenting our progress in developing this new system for sharing science and hope you’ll provide feedback.
Cells can be highly motile, moving in and out of a microscope’s field of view. Understanding complex life cycles is difficult without continuous observation. To overcome this challenge, we’ve developed a 3D-printed microchamber device to confine cells for long-term visualization.
Quantifying movement is a powerful window into cellular functions. However, cells can generate movement through a variety of complex mechanisms. Here, we generate a flexible framework for comparing an especially variable type of motility: cellular crawling.
The process of deciding whether a candidate actin homolog represents a “true” actin is tricky. We propose clear and data-driven criteria to define actin that highlight the functional importance of this protein while accounting for phylogenetic diversity.
Long protrusions from several microalgal species appear to help cells move, capture prey, transport mitochondria and chloroplasts, and more. Are they filopodia that evolved abilities more like other actin- or microtubule-based structures, or are they something new?
Prachee Avasthi, Cameron Dale MacQuarrie, and Atanas Radkov
PA
BB
Published: Mar 29, 2023
Treating P. tricornutum cells with serine endopeptidases or certain cytoskeletal inhibitors induces the formation of cell wall-free protoplasts and suggests a novel role for actin and myosin in preventing protoplast formation.
Even with many tools available, categorizing species is tough. We used data from Raman spectroscopy, a form of label-free imaging, to infer phylogenetic patterns among several dozen diverse microbial taxa, offering a non-destructive and rapid way to dissect species relationships.
Prachee Avasthi, Tara Essock-Burns, Galo Garcia III, Jase Gehring, David Q. Matus, David G. Mets, and Ryan York
PA
TE
+3
Published: May 03, 2023
Constraining motile microorganisms for live imaging often requires costly microfluidics or optical traps to keep them in view. We used patterned stamps and agar to make versatile, inexpensive “microchambers” and offer a way to predict the right chamber size for a given organism.
Prachee Avasthi, Rachel J. Dutton, Taylor Reiter, and Emily C.P. Weiss
PA
RD
KP
TR
Published: Jul 20, 2023
We are interested in neuroactive metabolites that influence animal behavior. Some fungi have horizontally transferred neuroactive metabolite pathways between species. We used a horizontal gene transfer detection pipeline to screen for novel fungal genes tied to neuroactivity.
Researchers studying any organism with genomic data can follow this simple walkthrough to create sets of barcoded probes for the multiplexed FISH technique called MERFISH. We’re sharing interactive code notebooks that can be adapted to design barcoded FISH probes for any species.
It is commonly assumed that phenotypes arise from the cumulative effects of many independent genes. However, we show that by accounting for dependent and nonlinear biological relationships, we can generate models that predict phenotypes with great accuracy.
Prachee Avasthi, Brae M. Bigge, Feridun Mert Celebi, Jase Gehring, Erin McGeever, Atanas Radkov, and Dennis A. Sun
PA
BB
RD
+12
Published: Sep 29, 2023
The ProteinCartography pipeline identifies proteins related to a query protein using sequence- and structure-based searches, compares all protein structures, and creates a navigable map that can be used to look at protein relationships and make hypotheses about function.
Prachee Avasthi, Feridun Mert Celebi, and Elizabeth A. McDaniel
PA
BB
+3
Published: Oct 06, 2023
Only some bacteria accumulate substantial amounts of polyphosphate (polyP). We thought that despite sequence divergence, polyP synthesis enzymes in these bacteria might have similar structures. We found this is sometimes true but doesn’t fully explain the phenomenon.
Prachee Avasthi, Ben Braverman, Tara Essock-Burns, Galo Garcia III, Cameron Dale MacQuarrie, David Q. Matus, David G. Mets, and Ryan York
PA
BB
TE
+7
Published: Jun 23, 2023
We’re crossing C. reinhardtii and C. smithii algae for high-throughput genotype-phenotype mapping. In preparation, we’re comparing the parents to uncover unique species-specific phenotypes.
Oligo pools can contain millions of unique sequences, but they’re limited by length, error rate, and bias. We propose methods to scalably screen synthetic DNA libraries, so an individual researcher can obtain thousands of error-free synthetic DNA assemblies at low cost.
Prachee Avasthi, Feridun Mert Celebi, Keith Cheveralls, Seemay Chou, Ilya Kolb, and David Q. Matus
PA
KC
SC
AH
+5
Published: Dec 02, 2023
Machine learning is a powerful tool for classifying images in a time series, such as the developmental stages of embryos. We built a classifier using only bright-field microscopy images to infer nematode embryonic stages at high throughput.