Biology subjects

Dey, G.

Publications and source records attributed to Dey, G..

At least 19 recordsLinked to original sources

bioRxiv2026

Concanavalin A as a pan-eukaryotic nuclear envelope marker for expansion microscopy

Across eukaryotes, the nuclear envelope exhibits distinct remodelling strategies during mitosis: complete breakdown (open mitosis), partial disruption (intermediate), or full retention (closed). However, both light and electron microscopy of the nuclear envelope, at sufficient resolution to determine integrity and mode of remodelling, have proven technically challenging. Here, Concanavalin A (ConA), a glycan-binding plant lectin, provides discernible nuclear envelope/endoplasmic reticulum (NE/ER) labelling in Ultrastructure Expansion Microscopy (U-ExM). Applied post-expansion, ConA circumvents antibody optimisation and labels the NE across mammalian cells and diverse microbial eukaryotes. By imaging four opisthokont and amoebozoan species with established mitotic strategies, C. perkinsii, D. discoideum, S. pombe, and S. arctica, we distinguished the full spectrum of NE remodelling. Applied to species with poorly characterised mitotic strategies, ConA revealed intermediate mitosis with polar fenestrae in the multinucleate stramenopile A. limacinum and a life cycle-coupled switch between open and closed mitosis in the amoebozoan P. polycephalum. These observations support the hypothesis that multinucleated life cycles favour closed or intermediate mitosis, protecting chromosomes from capture by neighbouring spindles during synchronous divisions. Together, these results establish ConA in combination with expansion microscopy as a broadly applicable tool for uncovering the diversity and evolution of NE remodelling across eukaryotes.

cell biology↗

bioRxiv2026

Septin-mediated coupling of protein import and division during chloroplast evolution

Chloroplast biogenesis depends on both protein import and organelle division, yet how their coordination emerged during evolution remains unclear. Here, we show that the single septin SEP1 links these pathways in the green alga Chlamydomonas reinhardtii. SEP1 forms a filamentous network on the chloroplast envelope during interphase and reorganizes into a ring at the chloroplast division site during cytokinesis. Loss of SEP1 selectively impairs import of chloroplast-division proteins and causes mispositioning of the division ring, without impairing bulk chloroplast protein import. SEP1 physically associates with outer-envelope TOC GTPases through evolutionarily related GTPase domains. Phylogenetic analysis places TOC GTPases within an algal septin-derived clade, and heterologous expression of SEP1 in land plants, in which septins are absent, shows conservation of its chloroplast targeting and TOC binding. Together, these findings identify septins as coordinators of plastid protein import and division and suggest that this coupling emerged early in chloroplast evolution.

cell biology↗

bioRxiv2026

A green fluorescent protein for live imaging in hyperthermophiles

Hyperthermophiles, organisms that thrive at temperatures above 60 {degrees}C, have played important roles in biotechnology and promise to reveal new biology. However, how these cells live remains poorly understood in part due to the lack of bright, thermostable fluorescent proteins that can be used to study protein localisation and dynamics at high temperatures. To overcome this challenge, here we describe the development of "Matcha", a green fluorescent protein that we have engineered from Thermal Green Protein by directed evolution in the thermophilic archaeon Sulfolobus acidocaldarius. The screen identified 7 mutations that when combined led to an [~]50-fold increase in the brightness of Matcha in vivo at physiological temperatures. Since this is sufficient for live cell imaging, we were then able to use Matcha-fusion proteins to study the division ring dynamics in Sulfolobus. Remarkably, this analysis reveals that, while ESCRT-III rings are disassembled as cells complete division, CdvA forms a stable polymeric ring that persists, and is asymmetrically inherited by one of the two daughter cells following cytokinesis. This study highlights the power of Matcha as a tool to shed light on our understanding of the cell biology of hyperthermophiles.

cell biology↗

bioRxiv2026

An Advanced Mobile Laboratory to enable field-based microbial ecology and cell biology across scales

Microbial biodiversity is central to ecosystem function, yet mechanistic insights into the cell biology of environmental organisms remain limited. The underlying challenges are twofold: most microbes remain uncultivable, and a persistent gap exists between field sampling and laboratory analyses. Here, we introduce the Advanced Mobile Laboratory (AML), a field-deployable platform that integrates confocal microscopy, image-enabled cell sorting, and cryo-preparation for expansion and electron microscopy. This setup enables immediate, standardized processing and analysis of environmental communities directly at the sampling site. We demonstrate its capability using marine eukaryotic plankton, showing how the AML enables multiscale investigations, from live imaging of natural communities to enabling ultrastructural and single-cell omics analyses, while minimizing sample degradation and enabling on-site experimentation. By bringing high-end sample preparation and analytical capacity into the field, the AML enables studying life in its natural context to mechanistically understand lifes diversity in the environment.

cell biology↗

bioRxiv2026

Microtubules sustain the fidelity of cellularization in a coenocytic relative of animals

Cellularization is the coordinated division of a multinucleate cytoplasm into many cells.1-3 Multinucleation is a common life cycle strategy observed across eukaryotic lineages, including in microbial eukaryotes, fungi, plants and animals, and is associated with the ability to transition to a unicellular state through cellularization.4 In the best-studied model for this process, Drosophila melanogaster, cellularization requires the coordinated action of actin and microtubule (MT) networks to bring about the synchronous invagination of plasma membrane furrows, but the extent of conservation of these mechanisms across eukaryotes remains unknown.1,5,6 Here we investigate cellularization in the ichthyosporean Sphaeroforma arctica, a close relative of animals with a multinucleate life cycle stage.7-9 Using live cell imaging, ultrastructure expansion microscopy (U-ExM) and volume electron microscopy, we define the membrane, MT and actin dynamics that accompany cellularization in S. arctica. Using pharmacological inhibitors and centrifugation, we show that MTs, in addition to positioning nuclei, play a role in guiding nascent furrows to sustain equi-partitioning of nuclei and cytoplasm between daughter cells. Our findings indicate that cellularization is regulated through crosstalk between actin and MT networks, exhibiting mechanistic parallels with canonical cytokinesis, and establish S. arctica as a valuable model for investigating general principles of cellularization.

cell biology↗

bioRxiv2025

A geothermal amoeba sets a new upper temperature limit for eukaryotes

The study of temperature limits has transformed our knowledge of the boundaries of life but has been largely focused on bacteria and archaea. We isolated a novel geothermal amoeba, Incendiamoeba cascadensis, that divides at 63{degrees}C (145.4{degrees}F), establishing a new record for the upper temperature limit across all eukaryotes. We demonstrated cellular proliferation with growth experiments and visualized mitosis via expansion microscopy. Using high-temperature live-cell imaging, we quantified movement up to 64{degrees}C. We assembled the genome of I. cascadensis and using comparative genomics found an enrichment of genes related to proteostasis, genome stability, and sensing the external environment. Taken together, our findings challenge the current paradigm of temperature constraints on eukaryotic cells and reshape our understanding of where and how eukaryotic life can persist.

microbiology↗

bioRxiv2025

Dystonia-associated Torsins sustain CLCC1 function to promote membrane fusion of the nuclear envelope for NPC biogenesis

DYT1 early-onset dystonia is a severe, incurable disorder of the central nervous system caused by mutations in the gene encoding Torsin1A (Tor1A, DYT1). Torsins are ER-resident AAA+-ATPases implicated in lipid metabolism, nuclear pore complex (NPC) biogenesis, and lipoprotein secretion, yet their molecular function that underlies the disease pathology has remained incompletely understood. Here, we have utilized Drosophila melanogaster and human somatic cells as experimental models to shed light on their mode-of-action. Fly germ cells lacking dTorsin are arrested in development and display defects in the final steps of NPC biogenesis due to a failure in fusion of the inner and outer nuclear membranes. Using proximity labelling of Torsin1A in human cells, we identify the conserved membrane protein chloride channel CLIC-like protein 1 (CLCC1) as a novel Torsin binding partner. Absence of human CLCC1 or its Drosophila homolog dClcc1 phenocopied the membrane fusion defects at NPC assembly sites observed upon Torsin deletion. Furthermore, CLCC1 is enriched at arrested fusion sites, suggesting it to be a candidate for the elusive NE membrane fusogen. Importantly, CLCC1/dClcc1 overexpression is sufficient to rescue NPC biogenesis and developmental defects associated with Torsin-loss-of-function. Taken together, our data suggest that Torsin-regulated CLCC1 activity drives membrane fusion during NPC biogenesis and reveal that modulating CLCC1 expression is a promising therapeutic prospect for DYT1 dystonia.

cell biology↗

bioRxiv2025

Environmental DNA Metabarcoding Effectively Detects Invasive Species, Pests, and Community Changes in Taiwan Rice Fields

Rice fields represent man-made semi-aquatic wetlands primed for invasive pests. Monitoring rice field biodiversity using conventional methods, however, is time-consuming and laborious. Environmental DNA (eDNA) methods can provide a fast and effective means to monitor rice field communities and inform management decisions. Our study provides proof-of-concept of rice field eDNA biodiversity assessments, with a focus on native and non-native pests across cultivation phases. We collected eDNA samples from locations in southern Taiwan during planting and harvesting, employing eDNA metabarcoding (COI) to detect diverse taxonomic groups. We assigned 77 ASVs across all sites to animal taxa, 34 of which were identified to species. Overall, 18 species were designated as native or non-native (83.3% and 16.6%, respectively), including three major rice pests, Chilo suppressalis (native), Coptotermes formosanus (native), and Pomacea canaliculata (non-native). Cultivation status affected overall diversity, with higher species richness during planting compared to harvesting. No significant differences were observed between native and non-native taxa between cultivation phases. Altogether, we detected a complex environment across trophic levels comprised of both native and non-native agricultural pests using limited sampling effort, demonstrating eDNA analysis as an efficient biomonitoring approach in rice agroecosystems with direct applications for pest, invasive species, and vector surveillance within Taiwan.

ecology↗

bioRxiv2025

Spatiotemporal control of cortical centrin patterning by regionalized Sfi1 family scaffolding proteins in Stentor coeruleus

Summary/AbstractPatterning is fundamental to the development and maintenance of organisms, ensuring functional and structural organization. While patterning is well studied at the level of multicellular organisms, even single cells need to undergo morphogenesis and form spatial patterns. Stentor coeruleus is a large ciliate that has been a classical system for studying patterning and morphogenesis due to its distinctive shape and organization of easily visible cortical structures which show a clear localization along the anterior-posterior body axis. The cortex of Stentor is made of two cytoskeletal layers, one composed of microtubules, and one composed of a network of centrin-family EF hand proteins, which form a branched network in the anterior half of the cell and long thick bundles known as myonemes in the posterior half. Sfi1 family proteins scaffold the assembly of centrin filaments throughout the eukaryotes, and function as scaffolding proteins in myonemal contractile systems found in some ciliates. A set of Sfi1 proteins upregulated during regeneration in Stentor were found to have a role in maintaining anterior/posterior differences in centrin patterning. Loss of this distinct anterior-posterior patterning leads to defects in regeneration and contraction. Using RNAi-mediated knockdown of Sfi1 genes, we have found that cells fail to regenerate their oral apparatus, with early expressed Sfi1 genes more critical for oral primordium (assembly of organized basal bodies that become the new oral apparatus) formation than those expressed later. Additionally, different Sfi1 proteins appear to be recruited sequentially to the growing primordium in an order that matches the time at which they are required for progression of regeneration. Knockdown of Sfi1 isoforms that results in reduced myoneme cables impairs contraction such that cells fail to contract in response to a stimulus or do not fully contract. These findings suggest a model in which regionalized differences in patterning of cytoskeletal assemblies can be modulated by regionalized localization of scaffolding proteins.

cell biology↗

bioRxiv2025

A conserved mechanism of membrane fusion in nuclear pore complex assembly

The nuclear pore complex (NPC) forms a large channel that spans the double lipid bilayer of the nuclear envelope and is the central gateway for macromolecular transport between the nucleus and cytoplasm in eukaryotes. NPC biogenesis requires the coordinated assembly of over 500 proteins culminating in the fusion of the inner and outer nuclear membranes. The molecular mechanism of this membrane fusion step that occurs in all eukaryotes is unknown. Here, we elucidate the mechanism by which two paralogous transmembrane proteins, Brl1 and Brr6, mediate membrane fusion in S. cerevisiae. Both proteins form multimeric, ring-shaped complexes with membrane remodeling activity. Brl1 is enriched at NPC assembly sites via a nuclear export sequence and then interacts with Brr6 across the nuclear envelope lumen through conserved hydrophobic loops. Disrupting this interaction blocks fusion and halts NPC assembly. Molecular dynamics simulations suggest that the Brl1-Brr6 complex drives membrane fusion by forming a channel across bilayers that enables lipid exchange. Phylogenetic analyses reveal that Brl1/Brr6 homologues are broadly distributed across eukaryotes, and functional experiments in human cells and D. melanogaster establish CLCC1 as an NPC fusogen in metazoans. Together, our results uncover a novel, conserved mechanism for membrane fusion in eukaryotes.

cell biology↗

bioRxiv2025

Diatom ultrastructural diversity across controlled and natural environments

Diatoms are ubiquitous aquatic microalgae critical to our planet, that were amongst the pioneer model organisms in cell biology for their large and transparent cell structure. However, their robust silica cell wall renders diatoms impermeable to many dyes and antibodies, and complicates the intracellular delivery of gene editing tools - driving in part the eventual decline of diatoms as mainstream model species despite their unique cellular physiology and remarkable ecological success. Here, we demonstrate that cryo-fixation combined with ultrastructural expansion microscopy (cryo-ExM) can overcome the silica barrier across diverse diatom species spanning over 80 million years of evolutionary time. We illustrate the potential of cryo-ExM to provide scalable, cost-effective volumetric imaging of diatom ultrastructure in laboratory cultures, as well as field-collected samples from the pan-European TREC expedition. We first reveal striking similarities in interphase microtubule organization across diverse diatom species by characterizing cytoskeletal arrangements throughout cell cycles and populations, uniting both pennate and centric morphologies under shared principles. We further unveil diatom photosynthetic diversity through qualitative and quantitative comparative analysis of chloroplast and pyrenoid morphologies, demonstrating that each diatom species architects unique photosynthetic machinery. Using cryo-ExM on environmental samples further exposes intricate diatom symbioses, revealing tight spatial organisation of ecological interactions. This methodology makes diatoms more accessible for modern and comparative cell biology research, providing new opportunities to investigate the cellular mechanisms of one of Earths most successful photosynthetic groups. HighlightsO_LICryo-ExM successfully overcomes diatom frustule barriers to achieve consistent, high-resolution immunofluorescence across evolutionarily diverse species - allowing for comparative cell biology in one of the most important phytoplankton groups on the planet. C_LIO_LICharacterizing microtubule organisation in asynchronously cycling single cells and colonial chains, reveals core features of interphase microtubule organisation across multiple pennate and centric diatom species. C_LIO_LIComparative analysis of chloroplast and pyrenoid morphologies across species provides qualitative and quantitative insights on photosynthetic diversity, suggesting that photosynthetic architectures are unique to each diatom. C_LIO_LIApplied to environmental samples, cryo-ExM provides detailed insight on spatial organisation of diatom symbioses. C_LI

cell biology↗

bioRxiv2025

Centromeres evolve progressively through selection at the kinetochore interface

During mitosis, stable but dynamic interactions between the centromere DNA and kinetochore complex enable accurate and efficient chromosome segregation. Even though many proteins of the kinetochore are highly conserved, centromeres are among the fastest evolving regions within a genome, showing extensive variation even on short evolutionary timescales. Here, we sought to understand how new types of centromeres emerge and reach fixation by mapping centromere evolution across 138 budding yeast species and over 2,500 natural strain isolates. We show that new centromeres spread progressively via drift and subsequent selection, and that the kinetochore interface, which is evolving slowly in relative terms, determines which new centromere variants are tolerated. Together, our findings provide insight into the evolutionary constraints and trajectories shaping centromere evolution.

evolutionary biology↗

bioRxiv2024

Harnessing Environmental DNA (eDNA) to Explore Frugivorous Interactions: A Case Study in Papaya (Carica papaya) and Pineapple (Ananas comosus)

Plant-animal interactions (PAIs) are critical in ecosystem function, mediating energy flow and species interactions. Traditional methods of tracking PAIs, such as morphological identification and camera trapping, are limited in speed and scalability, posing challenges for comprehensive biodiversity monitoring. Recently, environmental DNA (eDNA) metabarcoding has emerged as a promising technique for detecting species interactions non-destructively. This pilot study explores the application of eDNA metabarcoding to investigate interactions involving partially consumed and intact fruits of Carica papaya and Ananas comosus. eDNA metabarcoding were performed from of 36 partially consumed and 6 intact fruit samples. Metabarcoding of mitochondrial COI gene fragments revealed a diverse range of taxa, with Arthropoda, particularly insects, being the most abundant. Results indicated significant differences in taxonomic composition between pineapple and papaya samples, where both the fruit hold some unique as well as shared taxa. Furthermore, the diversity also differed between consumed and intact fruits, suggesting that partially consumed fruits serve as rich eDNA sources, capturing interactions with various frugivores and decomposers. Signal from various organisms detected through eDNA metabarcoding from consumed and damaged fruits allowed us to capture a wide array of taxa, revealing insights into species composition and ecological relationships. The unique ASVs associated with each fruit type suggest that certain taxa may showing preferences based on fruit characteristics such as sugar content, texture, or chemical profile. Present work highlighted the importance of eDNA based methods in unraveling the taxonomic composition of fruit-associated plant-animal interactions. This method needs limited taxonomic expertise, less labors, fast and effective, which can be implemented in monitoring ecological and economical species interactions.

ecology↗

bioRxiv2024

Charting the landscape of cytoskeletal diversity in microbial eukaryotes

Microbial eukaryotes are small and often resistant to standard labelling and imaging techniques, and therefore remain understudied - despite their critical ecological importance - with the exception of a few established models. Here, we use Ultrastructure Expansion Microscopy (U-ExM) to carry out high-resolution volumetric imaging of over 200 cultured planktonic eukaryotes across major lineages. By combining U-ExM with pan- and specific immuno-labelling, we reveal novel microtubule and centrin-containing elements and assign molecular identities to enigmatic cytoskeletal structures observed previously only by electron microscopy. Our investigation represents the first systematic survey of the extensive cytoskeletal diversity on display across the eukaryotic tree, including the major species groups of dinoflagellates, haptophytes, ciliates, euglenids, cryptomonads, and green algae. Our U-ExM approach extends to mixed environmental samples, paving the way for environmental cell biology at ultrastructural resolution and unprecedented scale, a crucial step towards understanding and protecting complex ecosystems in the face of biodiversity loss.

cell biology↗

bioRxiv2024

Expansion microscopy reveals unique ultrastructural features of pathogenic budding yeast species

Candida albicans is the most prevalent fungal pathogen isolated from patients with candidemia. As is the case for many other fungi, the complex life cycle of C. albicans has been challenging to study with high-resolution microscopy techniques due to its small size. We employed ultrastructure expansion microscopy (U-ExM) to directly visualise sub-cellular structures at high resolution in the C. albicans yeast and during its transition to hyphal growth. NHS-ester pan-labelling in combination with immunofluorescence (IF) provided the first comprehensive map of nucleolar and mitochondrial dynamics through the C. albicans cell cycle. Analysis of microtubules (MTs) and spindle pole bodies (SPBs) stained with marker proteins suggests that contrary to the pole-to-pole arrangement observed in Saccharomyces cerevisiae, C. albicans yeast cells display a unique side-by-side arrangement of SPBs with a short mitotic spindle and longer astral MTs (aMTs) at the pre-anaphase stage. Modifications to the established U-ExM protocol enabled the expansion of several medically relevant human fungal pathogens, revealing that the side-by-side SPB configuration is a plausible conserved feature shared by many fungal species. We highlight the power of U-ExM to investigate sub-cellular organisation and organellar dynamics at high resolution and low cost in poorly studied, medically relevant microbial pathogens.

cell biology↗

bioRxiv2024

The unseen invaders: tracking phylogeographic dynamics and genetic diversity of cryptic Pomacea canaliculata and P. maculata (Golden Apple Snails) across Taiwan

The cryptic invasion of golden apple snails (Pomacea canaliculata and P. maculata) in Taiwan has caused significant ecological and economical damage over last few decades, however, their management remains difficult due to inadequate taxonomic identification, complex phylogeny and limited population genetic information. We aim to understand the current distribution, putative population of origin, genetic diversity and potential path of cryptic invasion of Pomacea canaliculata and P. maculata across Taiwan to aid in improved mitigation approaches. The present investigation conducted a nationwide survey with 254 samples collected from 41 locations from 14 counties or cities across Taiwan. We identified P. canaliculata and P. maculata based on mitochondrial COI and compared their genetic diversity across Taiwan, as well as other introduced and native countries (based on publicly available COI data) to understand the possible paths of invasion in Taiwan. Based on mitochondrial COI barcoding, sympatric and heterogeneous distributions of invasive P. canaliculata and P. maculata were noted. Our haplotype analysis and mismatch distribution suggested multiple introductions of P. canaliculata in Taiwan was likely originated directly from Argentina, whereas P. maculata was probably introduced from a single, or a few, introduction event(s) from Argentina and Brazil. Our population genetic data further demonstrated a higher haplotype and genetic diversity for P. canaliculata and P. maculata in Taiwan compared to other introduced regions. Based on our current understanding, the establishment of P. canaliculata and P. maculata is alarming and widespread beyond geopolitical borders, requiring a concerted and expedited national and international invasive species mitigation program.

ecology↗

bioRxiv2023

Spindle architecture constrains karyotype in budding yeast

The eukaryotic cell division machinery must rapidly and reproducibly duplicate and partition the cells chromosomes in a carefully coordinated process. However, chromosome number varies dramatically between genomes, even on short evolutionary timescales. We sought to understand how the mitotic machinery senses and responds to karyotypic changes by using a series of budding yeast strains in which the native chromosomes have been successively fused. Using a combination of cell biological profiling, genetic engineering, and experimental evolution, we show that chromosome fusions are well tolerated up until a critical point. Cells with fewer than five centromeres lack the necessary number of kinetochore-microtubule attachments needed to counter outward forces in the metaphase spindle, triggering the spindle assembly checkpoint and prolonging metaphase. Our findings demonstrate that spindle architecture is a constraining factor for karyotype evolution.

cell biology↗

bioRxiv2023

Proteomic analysis reveals APOE isoform-specific regulation of ribosomes in neural precursor cells

ApoE4 isoform contributes to increased risk for Alzheimers Disease (AD) over the life course of individuals. Much remains unknown about the biological pathways that connect APOE4 genotype with the development of pathology that eventually leads to AD, nor do we know how early in life these cellular alterations begin. To answer these questions, we derived neural precursor cells (NPCs) from induced pluripotent stem cells (IPSCs) that were CRISPR-edited at the APOE locus. We intended to characterize the protein expression landscape in the NPCs subsequent to targeted deletion of E4 from a parent IPSC line of APOE3/4 genotype. Differentially expressed proteins (DEPs) following mass spectrometric analysis were determined from the protein abundance fold change values obtained for each protein. Proteins which showed >1.5-fold difference with FDR adjusted P-value < 0.05 were considered differentially expressed. DEPs were mapped to the STRING database (v11.5) for retrieval of interacting proteins and functional enrichment. CRISPR-editing of E4 from the parent line revealed 98 differential expressed proteins. Of these, 54 were upregulated, and 44 were downregulated. Further analysis of the DEPs via STRING database showed that these changes primarily affect pathways linked to RNA processing, plasma membrane repair, and cytoskeleton organization. Indeed, we find the effects of E4 extend beyond proteins considered central to AD pathology. Knowing more about the protein interactions regulated by ApoE, in an isoform-specific manner, can reveal new mechanistic insights into development of AD.

neuroscience↗