About

Professor Tobias Baskin leads research in the Baskin Lab within the Biology Department at the University of Massachusetts Amherst, focusing on growth and morphogenesis in plants. His research aims to understand anisotropic growth in plants by studying key cellular processes such as cell division, cell elongation, cortical microtubules, and cell wall properties. The lab employs a variety of techniques including electron, confocal, and light microscopy, molecular biology, growth kinetics analysis software, and drug studies to investigate these phenomena. Historically, the primary experimental material has been the plant root, but recent work has expanded to include tobacco BY2 cells. Additionally, Professor Baskin's research explores root physiology, particularly the relationships between cell division and expansion, with a focus on how the root of Arabidopsis thaliana acclimates to moderate temperatures.

Research topics

• Biology
• Mathematics
• Psychology
• Agronomy
• Biophysics
• Forestry
• Botany
• Materials science
• Social psychology
• Chemistry

Selected publications

• Observing biological spatio-angular structures and dynamics with statistical image reconstruction and polarized fluorescence microscopy

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-25

  preprintOpen access

  Understanding molecular orientation and density distributions is essential for exploring biological structure and function. Polarized fluorescence microscopy (PFM) provides insights into molecular architecture but struggles to resolve three-dimensional (3D) molecular orientation distributions, particularly in densely labeled or structurally complex specimens. To address this, we introduce the efficient generalized Richardson-Lucy (eGRL) algorithm, a robust framework for reconstructing 3D molecular density and orientation (spatio-angular) distributions from PFM data. By modeling the imaging process in spatio-angular hyperspace, we propose a maximum-likelihood solution enhanced by dimensionality reduction and angular domain transformation to overcome computational challenges. eGRL improves accuracy and efficiency across different PFM implementations, enabling use on standard platforms. We utilize our methods to resolve biological spatio-angular structures and dynamics otherwise impossible to resolve, including the tangential alignment of actin filaments in U2OS cells, nanowire-guided cytoskeletal organization in NIH3T3 cells, rotational actin patterns in live HeLa protrusions, and membrane tension-induced anisotropy in live macrophages.

  PublisherOA PDFDOI

• Volumetric imaging of the 3D orientation of cellular structures with a polarized fluorescence light-sheet microscope

  Proceedings of the National Academy of Sciences · 2025-02-21 · 6 citations

  articleOpen access

  Polarized fluorescence microscopy is a valuable tool for measuring molecular orientations in biological samples, but techniques for recovering three-dimensional orientations and positions of fluorescent ensembles are limited. We report a polarized dual-view light-sheet system for determining the diffraction-limited three-dimensional distribution of the orientations and positions of ensembles of fluorescent dipoles that label biological structures. We share a set of visualization, histogram, and profiling tools for interpreting these positions and orientations. We model the distributions based on the polarization-dependent efficiency of excitation and detection of emitted fluorescence, using coarse-grained representations we call orientation distribution functions (ODFs). We apply ODFs to create physics-informed models of image formation with spatio-angular point-spread and transfer functions. We use theory and experiment to conclude that light-sheet tilting is a necessary part of our design for recovering all three-dimensional orientations. We use our system to extend known two-dimensional results to three dimensions in FM1-43-labeled giant unilamellar vesicles, fast-scarlet-labeled cellulose in xylem cells, and phalloidin-labeled actin in U2OS cells. Additionally, we observe phalloidin-labeled actin in mouse fibroblasts grown on grids of labeled nanowires and identify correlations between local actin alignment and global cell-scale orientation, indicating cellular coordination across length scales.

  PublisherDOI

• The three cellulose synthase isoforms for secondary cell wall make specific contributions to microfibril synthesis

  The Plant Journal · 2025-07-01

  articleSenior authorCorresponding

  Cellulose is synthesized at the plasma membrane by the cellulose synthase complex, a structure that contains three distinct isoforms of the catalytic subunit, cellulose synthase A (CESA). The division into three subunits appears early in land plant evolution and is highly conserved, particularly for the secondary cell wall. However, what if any unique roles each isoform plays in the complex remain unclear. Here, we assessed the contributions of specific isoforms to microfibril synthesis. First, we expressed CESA isoforms of the primary cell wall or the moss Physcomitrium patens in Arabidopsis thaliana backgrounds missing a secondary cell wall CESA. While the primary cell wall isoforms rescued the cesa knockout phenotype with partial isoform specificity, those from the moss rescued with fewer restrictions. Then, we recreated various CESA missense mutations in all three of the secondary cell wall isoforms; while results are consistent with isoform specificity, they are difficult to interpret further without molecular structures. Finally, we show that catalytically inactive CESA isoforms restore growth and cellulose content in the corresponding knockout in an isoform-specific manner; along with partial rescue of the growth and cellulose content of the inflorescence stem, the replacement lines have fiber cells with partially disorganized microfibrils and secondary cell wall cellulose with narrow crystal width. Generally, effects were more pronounced in lines where CESA8 was inactivated compared with inactivating CESA4 or 7, which tended to have similar phenotypes to each other. We account for these results with a model for cellulose synthase structure with the isoforms assigned specific localization within the cellulose synthase complex.

  PublisherDOI

• Thermomorphogenesis of the <i>Arabidopsis thaliana</i> Root: Flexible Cell Division, Constrained Elongation and the Role of Cryptochrome

  Plant and Cell Physiology · 2024-07-20 · 6 citations

  articleSenior author

  Understanding how plants respond to temperature is relevant for agriculture in a warming world. Responses to temperature in the shoot have been characterized more fully than those in the root. Previous work on thermomorphogenesis in roots established that for Arabidopsis thaliana (Columbia) seedlings grown continuously at a given temperature, the root meristem produces cells at the same rate at 15°C as at 25°C and the root's growth zone is the same length. To uncover the pathway(s) underlying this constancy, we screened 34 A. thaliana genotypes for parameters related to growth and division. No line failed to respond to temperature. Behavior was little affected by mutations in phytochrome or other genes that underly thermomorphogenesis in shoots. However, a mutant in cryptochrome 2 was disrupted substantially in both cell division and elongation, specifically at 15°C. Among the 34 lines, cell production rate varied extensively and was associated only weakly with root growth rate; in contrast, parameters relating to elongation were stable. Our data are consistent with models of root growth that invoke cell non-autonomous regulation for establishing boundaries between meristem, elongation zone and mature zone.

  PublisherDOI

• Three-dimensional spatio-angular fluorescence microscopy with a polarized dual-view inverted selective-plane illumination microscope (pol-diSPIM)

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-03-12 · 3 citations

  preprintOpen access

  Polarized fluorescence microscopy is a valuable tool for measuring molecular orientations, but techniques for recovering three-dimensional orientations and positions of fluorescent ensembles are limited. We report a polarized dual-view light-sheet system for determining the three-dimensional orientations and diffraction-limited positions of ensembles of fluorescent dipoles that label biological structures, and we share a set of visualization, histogram, and profiling tools for interpreting these positions and orientations. We model our samples, their excitation, and their detection using coarse-grained representations we call orientation distribution functions (ODFs). We apply ODFs to create physics-informed models of image formation with spatio-angular point-spread and transfer functions. We use theory and experiment to conclude that light-sheet tilting is a necessary part of our design for recovering all three-dimensional orientations. We use our system to extend known two-dimensional results to three dimensions in FM1-43-labelled giant unilamellar vesicles, fast-scarlet-labelled cellulose in xylem cells, and phalloidin-labelled actin in U2OS cells. Additionally, we observe phalloidin-labelled actin in mouse fibroblasts grown on grids of labelled nanowires and identify correlations between local actin alignment and global cell-scale orientation, indicating cellular coordination across length scales.

  PublisherOA PDFDOI

• Mother trees, altruistic fungi, and the perils of plant personification

  Trends in Plant Science · 2023 · 35 citations

  • Biology
  • Psychology
  • Social psychology
  PublisherDOI

• <scp><i>BUZZ</i></scp>: an essential gene for postinitiation root hair growth and a mediator of root architecture in <i>Brachypodium distachyon</i>

  New Phytologist · 2023-07-08 · 5 citations

  articleOpen access

  Here, we discover a player in root development. Recovered from a forward-genetic screen in Brachypodium distachyon, the buzz mutant initiates root hairs but they fail to elongate. In addition, buzz roots grow twice as fast as wild-type roots. Also, lateral roots show increased sensitivity to nitrate, whereas primary roots are less sensitive to nitrate. Using whole-genome resequencing, we identified the causal single nucleotide polymorphism as occurring in a conserved but previously uncharacterized cyclin-dependent kinase (CDK)-like gene. The buzz mutant phenotypes are rescued by the wild-type B. distachyon BUZZ coding sequence and by an apparent homolog in Arabidopsis thaliana. Moreover, T-DNA mutants in A. thaliana BUZZ have shorter root hairs. BUZZ mRNA localizes to epidermal cells and develops root hairs and, in the latter, partially colocalizes with the NRT1.1A nitrate transporter. Based on qPCR and RNA-Seq, buzz overexpresses ROOT HAIRLESS LIKE SIX-1 and -2 and misregulates genes related to hormone signaling, RNA processing, cytoskeletal, and cell wall organization, and to the assimilation of nitrate. Overall, these data demonstrate that BUZZ is required for tip growth after root hair initiation and root architectural responses to nitrate.

  PublisherOA PDFDOI

• Cellulose assembles into helical bundles of uniform handedness in cell walls with abnormal pectin composition

  The Plant Journal · 2023-08-07 · 10 citations

  articleOpen access

  Plant cells and organs grow into a remarkable diversity of shapes, as directed by cell walls composed primarily of polysaccharides such as cellulose and multiple structurally distinct pectins. The properties of the cell wall that allow for precise control of morphogenesis are distinct from those of the individual polysaccharide components. For example, cellulose, the primary determinant of cell morphology, is a chiral macromolecule that can self-assemble in vitro into larger-scale structures of consistent chirality, and yet most plant cells do not display consistent chirality in their growth. One interesting exception is the Arabidopsis thaliana rhm1 mutant, which has decreased levels of the pectin rhamnogalacturonan-I and causes conical petal epidermal cells to grow with a left-handed helical twist. Here, we show that in rhm1 the cellulose is bundled into large macrofibrils, unlike the evenly distributed microfibrils of the wild type. This cellulose bundling becomes increasingly severe over time, consistent with cellulose being synthesized normally and then self-associating into macrofibrils. We also show that in the wild type, cellulose is oriented transversely, whereas in rhm1 mutants, the cellulose forms right-handed helices that can account for the helical morphology of the petal cells. Our results indicate that when the composition of pectin is altered, cellulose can form cellular-scale chiral structures in vivo, analogous to the helicoids formed in vitro by cellulose nano-crystals. We propose that an important emergent property of the interplay between rhamnogalacturonan-I and cellulose is to permit the assembly of nonbundled cellulose structures, providing plants flexibility to orient cellulose and direct morphogenesis.

  PublisherOA PDFDOI

• The <i>miR156</i> juvenility factor and <i>PLETHORA 2</i> form a regulatory network and influence timing of meristem growth and lateral root emergence

  Development · 2022-10-25 · 6 citations

  articleOpen access

  Plants develop throughout their lives: seeds become seedlings that mature and form fruits and seeds. Although the underlying mechanisms that drive these developmental phase transitions have been well elucidated for shoots, the extent to which they affect the root is less clear. However, root anatomy does change as some plants mature; meristems enlarge and radial thickening occurs. Here, in Arabidopsis thaliana, we show that overexpressing miR156A, a gene that promotes the juvenile phase, increased the density of the root system, even in grafted plants in which only the rootstock had the overexpression genotype. In the root, overexpression of miR156A resulted in lower levels of PLETHORA 2, a protein that affects formation of the meristem and elongation zone. Crossing in an extra copy of PLETHORA 2 partially rescued the effects of miR156A overexpression on traits affecting root architecture, including meristem length and the rate of lateral root emergence. Consistent with this, PLETHORA 2 also inhibited the root-tip expression of another miR156 gene, miR156C. We conclude that the system driving phase change in the shoot affects developmental progression in the root, and that PLETHORA 2 participates in this network.

  PublisherDOI

• Peer Review #1 of "Ethylene represses the promoting influence of cytokinin on cell division and expansion of cotyledons in etiolated Arabidopsis thaliana seedlings (v0.1)"

  2022-10-31

  peer-reviewOpen accessCorresponding

  The plant hormones ethylene and cytokinin influence many processes; sometimes they act cooperatively, other times antagonistically.To study their antagonistic interaction, we used the cotyledons of etiolated, intact seedlings of Arabidopsis thaliana.We focused on cell division and expansion, because both processes are quantified readily in paradermal sections.Here, we show that exogenous cytokinins modestly stimulate cell division and expansion in the cotyledon, with a phenyl-urea class compound exerting a larger effect than benzyl-adenine.Similarly, both processes were stimulated modestly when ethylene response was inhibited, either chemically with silver nitrate or genetically with the eti5 ethylene-insensitive mutant.However, combining cytokinin treatment with ethylene insensitivity was synergistic, strongly stimulating both cell division and expansion.Evidently, ethylene represses the growth promoting influence of cytokinin, whether endogenous or applied.We suggest that the intact etiolated cotyledon offers a useful system to characterize how ethylene antagonizes cytokinin responsiveness.

  PublisherOA PDFDOI

Recent grants

• Regulation of Division and Elongation During Root Growth

  NSF · $485k · 2003–2007

• Collaborative Research and RUI: Auxin Fluxes in the Arabidopsis Root Apex--a Combined Experimental and Computational Approach

  NSF · $102k · 2008–2013

• Collaborative Research: Dynamic zonation in the plant root

  NSF · $565k · 2021–2026

Frequent coauthors

• Hari Shroff

  Janelia Research Campus

  10 shared

• Winslow R. Briggs

  Department of Plant Biology

  10 shared

• Eric M. Kramer

  Bard College at Simon's Rock

  9 shared

• Moritoshi Iino

  Osaka City University

  9 shared

• Kannappan Palaniappan

  University of Missouri

  9 shared

• Yijun Su

  National Institutes of Health

  8 shared

• Heidi L. Rutschow

  7 shared

• Alex Bannigan

  University of Massachusetts Amherst

  7 shared

Education

• B.S.

  Yale

  1980

• Ph.D.

  Stanford University

  1986

• Other, Postdoctoral

  University of California, Berkeley

  1987

• Other, Postdoctoral

  Australian National University

  1990