Biology subjects

Dubey, A.

Publications and source records attributed to Dubey, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Scalable hardware and software for high-density, multi-regional electrophysiology in non-human primates

Understanding how distributed neural circuits generate complex behaviors requires long-duration recordings from populations of individual neurons across multiple brain regions. High-density Neuropixels probes have revolutionized rodent systems neuroscience. Extending these capabilities to non-human primates (NHPs) for chronic, multi-regional recordings requires compact, implantable microdrive hardware and reliable automated spike-sorting software. NHPs provide access to complex and flexible behaviors that are difficult to study in other model systems. Extending the Neuropixels revolution to NHPs therefore depends on integrating hardware and software for long-duration, multi-regional recordings. Here, we present a scalable hardware-software platform co-designed for high-density neural data acquisition and reliable single-unit identification in NHPs. The Multi-regional Implantable NeuroDrive (MIND) is a lightweight, implantable microdrive that provides stable recordings from multiple independently positioned Neuropixels probes and is designed to support chronic, ambulatory, head-free recordings. We paired MIND with UnitAssay, an automated post-sorting curation framework that identifies and curates characteristic spike-sorting errors with minimal computational cost. Together, MIND and UnitAssay provide an integrated platform for implanted, multi-regional recordings in NHPs performing complex and naturalistic behaviors. We tested MIND and UnitAssay across parietal, prefrontal, and motor cortices in rhesus macaques performing reaching and eye-movement tasks. MIND enabled stable multi-probe recordings across cortical regions and durations. UnitAssay enabled automated curation of large-scale spike-sorting output and improved reliable single-unit identification relative to Kilosort 4 labels and standard SpikeInterface quality control. Together, MIND and UnitAssay provide a scalable solution for high-density, multi-regional, long-duration electrophysiology in NHPs.

neuroscience↗

bioRxiv2026

Chaperonin recognition of protein dynamics drives drug resistance

The emergence of drug resistance is typically driven by mutations that alter drug-target affinity, yet the role of host cellular machinery regulating these processes remains unclear. Here, we reveal that the chaperonin GroEL/S promotes drug resistance through recognition of protein dynamics. Using directed evolution of E. coli DHFR under antibiotic stress and varying GroEL/S expression, we identify a well-folded resistance variant whose fitness, despite tight inhibitor binding, is critically potentiated by GroEL/S engagement. X-ray crystallography, NMR, molecular dynamics and kinetic modeling reveal that millisecond-timescale flipping of the M20 loop generates steric accessibility and a kinetic window for chaperonin interaction that forcibly displaces tightly bound inhibitors, thereby overriding thermodynamic equilibrium of inhibitor binding to restore the active enzyme pool and preserve metabolic flux. Our findings not only reveal a novel paradigm of "dynamic recognition" where both conformational kinetics and distribution govern chaperonin recognition but also establish chaperonins as "deligandases" that actively modulate in vivo drug binding, suggesting that chaperone surveillance of the cellular proteome extends beyond quality control to govern native protein function. This mechanism defines a previously unrecognized route for the rapid development of drug resistance, with implications for understanding therapeutics of microbial infections and human malignancies.

biophysics↗

bioRxiv2026

Early evolution of the prokaryotic transcription factor repertoire

Transcription initiation is regulated by proteins called transcription factors (TFs). Though TFs help determine phenotype across the tree of life, they are nonessential for minimal cellular life and are often absent in endosymbiotic and parasitic organisms. Given this and the idea that it is a certain level of organism complexity that calls for specific transcription regulation, we traced the evolutionary history of TF repertoire on a bacterio-archaeal tree of life using a dataset of [~]500,000 TFs, grouped into [~]1,700 orthologous groups (OGs) across [~]3,000 species. The most ancestral prokaryotes encoded multiple TFs. Going by known extant functions of these TFs, they possibly regulated sugar-fermentation metabolism, sensed overall metabolic state and redox, responded to DNA damage or bound metals; many of which are consistent with some reconstructions of ancestral gene pools and physiologies. The number of TFs as well as their superfamily-level diversity, through evolutionary history, matches expectations against genome size derived from extant bacteria, suggesting pre-LUCA diversification of TF sequence families. Emergence of new TFs along the phylogeny largely followed a smooth cumulative distribution curve, suggesting steady innovation, early in prokaryote evolution, in contrast to eukaryotes, in which a majority of TF families emerged in a burst manner at the ancestors of multicellular lineages. Gains of TFs late in prokaryotic evolution predominantly featured recycling of protein families discovered elsewhere in the prokaryotic tree, consistent with the dominance of horizontal gene transfer in these organisms. We speculate on the difference between the evolutionary trajectory of prokaryotic TF repertoire and compare it with the eukaryotic TF repertoire trajectory. This helps us in understanding the manner in which their TF repertoires have evolved in two different super-kingdoms. The difference between the evolutionary dynamics of TF-repertoires might be due to how complexity is envisioned in these two different kingdoms.

evolutionary biology↗

bioRxiv2025

Activin/TGF-beta signaling levels coordinate whole-body regeneration with genotoxic stress in Schmidtea mediterranea

Highly regenerative animals often have a seemingly limitless capacity for tissue growth and stem cell proliferation, which often requires molecular and organismal capacities associated with pre-malignancy. Yet, these same organisms do not develop stem cell driven cancers. Here, we explored if the regenerative flatworm Schmidtea mediterranea has evolved mechanisms to modulate regeneration depending on underlying DNA damage or neoplastic risk. We first challenged worms to regenerate after increasing doses of ionizing radiation and found that even sublethal doses (500-1250Rads) transiently inhibit regeneration. After amputation, stem cells could divide and accumulate near injuries but did not increase proliferation rates in response to amputation or restore missing tissues. By leveraging published single cell sequencing datasets, we found that ionizing radiation increased activin ligand expression, particularly in the intestine. RNAi knockdown of 18 different activin signaling homologs identified activin ligands, activin receptors, and downstream Smad transcription factors whose depletion partially or fully rescued regenerative capacity after radiation. Notably, depletion of activin-2 did not alter radiation-induced stem cell loss. Instead, it increased stem cell expansion and amputation-induced proliferation, fully restoring regeneration despite prior DNA damage and depleted stem cell numbers. Together, our results indicate that Activin signaling levels are a central regulator of planarian stem cell behaviors, coordinating shifts between repair of pre-existing tissues following systemic damage, homeostatic tissue turnover, and whole-body regeneration. Moreover, Activin signaling may function as a conserved tumor suppressor in Schmidtea mediterranea by inhibiting stem-cell driven regeneration when damage levels are too high. In BriefBrownlee et al. uncover an activin/TGF-beta dependent inhibition of regenerative capacity following ionizing radiation in the highly regenerative flatworm Schmidtea mediterranea. While activin depletion had little effect on irradiation-induced stem cell loss, it significantly increased stem cell expansion and proliferation when irradiated worms were amputated, restoring regeneration despite reduced stem cell numbers. HighlightsO_LISub-lethal exposures of ionizing radiation transiently inhibit regenerative ability in the planarian Schmidtea mediterranea C_LIO_LIIonizing radiation does not prevent surviving stem cells from dividing but reduces their ability to increase proliferation rates and regenerate missing tissues after amputation. C_LIO_LIDepletion of different Activin/TGF-beta signaling components rescues regenerative capacity after irradiation C_LIO_LIHeightened stem cell expansion and amputation-induced proliferation underlie increased regenerative capacity upon activin depletion C_LI

developmental biology↗

bioRxiv2025

Transcriptional control of neuronal maintenance by SOX2 during inner ear innervation

The cochlear sensory epithelium and the spiral ganglion neurons it supports arise from a common pool of otic progenitors, yet the neurons remain dependent on the epithelium for guidance and survival long after the two lineages diverge. How that dependency is sustained as the progenitor pool generates increasingly restricted cell types is unknown. Here we show that SOX2 maintains this regulatory continuity. Deletion of Sox2 from the cochlear epithelium after cochlear neurogenesis does not affect neuroblast generation, delamination and proliferation; however, peripheral axons failed to reach the epithelium and neurons were progressively lost, identifying a non-cell-autonomous requirement for epithelial SOX2. Transcriptomic profiling revealed a SOX2-dependent epithelial programme enriched for neurotrophic and axon-guidance genes, including Ntf3 and Bdnf. In cochlear organoids, acute Sox2 deletion reduced H3K27ac at regulatory elements while H3K4me1 remained stable, consistent with SOX2 maintaining the activity of previously marked enhancers. Ntf3 and Bdnf exemplified distinct regulatory trajectories. At Ntf3, SOX2 occupied an enhancer whose activity depended on Sox2, whereas at Bdnf it occupied promoter-proximal elements in progenitors before ATOH1 engaged these and a hair-cell-active distal enhancer. Thus, SOX2 links sensory fate specification to epithelial-neuronal communication. More generally, our findings suggest that regulatory competence can persist through lineage restriction, while changing transcription-factor inputs partition its output among descendants to coordinate their development.

developmental biology↗

bioRxiv2025

Commensal taxa in gut microbiota limit antibiotic resistance during extended oral antibiotic use

Certain bacterial infections, such as those involving prosthetics, can require antimicrobial therapy over months to years, potentially increasing the burden of antimicrobial resistance. Here we longitudinally track the antimicrobial resistome in mice during continuous antibiotic dosing over 21 months. The burden of antibiotic resistance genes (ARGs) initially increases, but, surprisingly, declines in later months, approaching levels observed in untreated animals. ARG burden is regulated by taxonomy and declines as ARG-harboring taxa that initially bloom are replaced by commensals. Furthermore, we find that the dynamics of antibiotic-induced ARG burden are influenced by age-related differences in microbial taxonomy and can be removed by fecal microbiota transplantation. We show that commensals may regulate the resistome by limiting the growth of ARG-harboring taxa, thereby providing antimicrobial expansion resistance.

microbiology↗

bioRxiv2025

Bio-sintering of Limestone to Produce Pollution Free Cement

Industrial cement is produced by consuming too much energy and emitting very high CO2. Nature too produces cement, but it is pollution-free. This research demonstrates an emulation of natural cement by bio-sintering limestone, a process of successive dissolution and reprecipitation of limestone with the help of bacteria in ambient environmental conditions. When the bacteria Acetobacter aceti were introduced into a mixture of ethanol and limestone powder, the pH came down rapidly, and dissolution of limestone into calcium acetate was observed. After the ethanol was fully consumed, the pH rose gradually, and biocement crystals were reprecipitated. All the reaction rates have been determined, and the products have been characterised. It is observed that the morphology of the biocement could be tailored by controlling the reprecipitation process. The dissolution and reprecipitation took place within the time scale of present construction methods. Thus, this process can potentially manufacture industrial cement from limestone sans the pollution.

bioengineering↗

bioRxiv2025

Disrupting Viral Replication in Human Metapneumovirus: Targeting Key Proteins with Unani Phytochemicals through Structural Dynamics and Energetics

Emerging viral infections pose significant global health challenges, necessitating the exploration of novel antiviral therapeutics. This study investigates the antiviral potential of bioactive compounds derived from the Unani system of medicine, leveraging molecular docking, molecular dynamics simulations, pharmacokinetic profiling, and quantum chemical calculations to assess their efficacy against the Human Metapneumovirus (HMPV) target protein (PDB ID: 5WB0).Molecular docking studies revealed that Crocin (-9.5 kcal/mol), Quercetin (-9.3 kcal/mol), and Oleuropein (-9.0 kcal/mol) exhibited remarkable binding affinities, engaging in multiple hydrogen bonds and hydrophobic interactions, comparable to standard antiviral drugs Remdesivir (-9.2 kcal/mol) and Favipiravir (-8.8 kcal/mol). These findings were further supported by molecular dynamics simulations, where Crocin and Quercetin maintained exceptional binding stability (RMSD ~1.8 [A], MM-PBSA energy ~ -80.5 kcal/mol), reinforcing their potential as HMPV inhibitors.Additionally, pharmacophore modeling and electronic structure analysis highlighted strong hydrogen bonding capacity, dipole moment, and electrostatic potential for these bioactives, facilitating optimal target interactions. Pharmacokinetic and toxicological assessments confirmed their high bioavailability, metabolic stability, and minimal toxicity, positioning them as promising candidates for further drug development.Overall, this comprehensive computational study underscores the therapeutic relevance of Unani-derived compounds, paving the way for natural antiviral interventions. Future in vitro and in vivo investigations will be essential to validate their clinical efficacy and optimize their drug-like properties.

bioinformatics↗

bioRxiv2025

Unlocking Antiviral Potentials of Traditional Plants: A Multi-Method Computational Study against Human Metapneumovirus (HMPV)

Human metapneumovirus (HMPV) remains a critical challenge in respiratory healthcare, particularly due to the lack of targeted antiviral therapies and vaccines. This study employs an integrative computational framework to identify and evaluate the antiviral potential of nature-based compounds derived from traditional medicinal plants. A suite of advanced methodologies, including virtual screening, molecular docking, molecular dynamics (MD) simulations, density functional theory (DFT) calculations, pharmacophore modeling, and ADMET profiling, was utilized to comprehensively analyze candidate compounds. Among the tested compounds, Glycyrrhizin exhibited exceptional properties, with a binding energy of -65.4 kcal/mol, eight stabilizing hydrogen bonds, and remarkable dynamic stability (RMSD 1.3 [A]). Similarly, Withaferin A demonstrated a binding energy of -63.7 kcal/mol and high pharmacokinetic potential. Quantum-level analyses revealed favorable electronic properties, while ADMET profiling confirmed the compounds safety and drug-like characteristics. These findings underscore the potential of traditional phytochemicals to serve as lead candidates in antiviral drug development. This research bridges the gap between traditional medicine and modern computational techniques, paving the way for innovative and efficient therapeutic strategies against HMPV.

bioinformatics↗

bioRxiv2025

Exploring FDA-Approved Antiviral Drugs for Human Metapneumovirus Treatment: Integrative Computational Insights

This study leverages advanced computational methodologies to identify potential antiviral therapies targeting human metapneumovirus (HMPV), focusing on FDA-approved antiviral drugs and control compounds. A comprehensive computational framework, encompassing virtual screening, molecular docking, molecular dynamics (MD) simulations, density functional theory (DFT) analysis, and ADMET profiling, was employed. Key findings highlight Remdesivir and Peramivir as the most promising candidates, with superior binding energies (-9.5 kcal/mol and - 9.2 kcal/mol, respectively), stable interaction profiles, and robust pharmacological properties. Molecular dynamics revealed exceptional stability for Remdesivir, with the lowest RMSD (0.20 nm), and pharmacophore analysis emphasized its strong hydrogen bonding and hydrophobic interactions. ADMET profiling confirmed their high bioavailability (85% {+/-} 3 for Remdesivir) and low toxicity, positioning these drugs for repurposing against HMPV. This integrative study underscores the potential of computational tools in streamlining drug discovery and advancing therapeutic interventions.

bioinformatics↗

bioRxiv2025

Repurposing Metal-Based Therapeutics for Human Metapneumovirus (HMPV): An Integrative Computational Approach

Human metapneumovirus (HMPV) poses a significant global health challenge, with limited therapeutic options available. This study employs a comprehensive computational framework to repurpose metal-based drugs as potential HMPV inhibitors. A library of compounds was systematically evaluated using virtual screening, high-precision molecular docking, molecular dynamics (MD) simulations, density functional theory (DFT) calculations, molecular electrostatic potential (MESP) mapping, and pharmacophore modeling. Key candidates, including Auranofin, Silver Sulfadiazine, and Gallium Nitrate, demonstrated high binding affinities ({Delta}Gbinding: -68.5 to -62.7 kcal/mol) and favorable stability metrics (RMSD: 2.1-2.4 [A]). ADME-toxicity (ADMET) profiling highlighted Auranofins robust bioavailability (80%) and extended half-life (8.5 hours), while Ribavirin and Favipiravir emerged as safe controls with minimal toxicity. Quantum chemical analyses reinforced the compounds electronic stability and reactivity. This integrative study provides a promising avenue for repurposing existing therapeutics, bridging computational insights with translational potential to combat HMPV.

bioinformatics↗

bioRxiv2025

Harnessing Computational Insights to Identify Potent Inhibitors for Human Metapneumovirus (HMPV): A Synergistic Approach with Natural Compounds

Human metapneumovirus (HMPV), a leading cause of acute lower respiratory tract infections, has emerged as a global health challenge due to its high prevalence, particularly among children, the elderly, and immunocompromised individuals. Despite its significant impact, no targeted antivirals or vaccines are available. This study employs a comprehensive computational pipeline to identify and evaluate potential inhibitors of the HMPV matrix protein (PDB: 5WB0). Natural compounds such as epigallocatechingallate (EGCG), rutin, and quercetin, along with control drugs, were screened for their therapeutic potential.Virtual screening identified EGCG (-9.1 kcal/mol), rutin (-9.0 kcal/mol), and quercetin (-8.8 kcal/mol) as top binders, surpassing standard drugs like ribavirin (-8.9 kcal/mol). Molecular docking revealed stable binding interactions, including hydrogen bonding with residues Arg143 and Glu186. Molecular dynamics (MD) simulations over a 1000 ns trajectory confirmed the stability of these complexes, with EGCG displaying the lowest RMSD (2.1 [A]) and consistent hydrogen bonding throughout the simulation. Density Functional Theory (DFT) calculations highlighted favorable electronic properties, with EGCG showing a low band gap (3.29 eV) and high dipole moment (3.12 D), indicative of strong reactivity and binding potential. ADMET profiling revealed excellent oral bioavailability for EGCG (84%) and quercetin (88%), with minimal toxicity risks. The Molecular Electrostatic Potential (MESP) mapping identified highly reactive regions on the molecular surface, correlating with nucleophilic and electrophilic binding capabilities. The findings position EGCG, rutin, and quercetin as promising candidates for HMPV therapy, providing a strong foundation for further experimental validation and preclinical development.

bioinformatics↗

bioRxiv2024

Evolution of transcription factor-containing superfamilies in Eukaryotes

Regulation of gene expression helps determine various phenotypes in most cellular life forms. It is orchestrated at different levels and at the point of transcription initiation by transcription factors (TFs). TFs bind to DNA through domains that are evolutionarily related, by shared membership of the same superfamilies (TF-SFs), to those found in other nucleic acid binding and protein-binding functions (nTFs for non-TFs). Here we ask how TF DNA binding sequence families in eukaryotes have evolved in relation to their nTF relatives. TF numbers scale by power law with the total number of protein-coding genes differently in different clades, with fungi usually showing sub-linear powers whereas chordates show super-linear scaling. The LECA probably encoded a complex regulatory machinery with both TFs and nTFs, but with an excess of nTFs when compared to the relative distribution of TFs and nTFs in extant organisms. Losses drive the evolution of TFs and nTFs, with the possible exception of TFs in Animalia for some tree topologies. TFs are highly dynamic in evolution, showing higher gain and loss rates than nTFs though both are conserved to similar extents. Gains of TFs and nTFs are driven by the appearance of a large number of new sequence clusters in a small number of nodes, which determine the presence of as many as a third of extant TFs and nTFs as well as the relative presence of TFs and nTFs. Whereas nodes showing explosion of TF numbers belong to multicellular clades, those for nTFs lie among the fungi and the protists.

genomics↗

bioRxiv2024

Stable, chronic in-vivo recordings from a fully wireless subdural-contained 65,536-electrode brain-computer interface device

Minimally invasive, high-bandwidth brain-computer-interface (BCI) devices can revolutionize human applications. With orders-of-magnitude improvements in volumetric efficiency over other BCI technologies, we developed a 50-m-thick, mechanically flexible micro-electrocorticography (ECoG) BCI, integrating a 256x256 array of electrodes, signal processing, data telemetry, and wireless powering on a single complementary metal-oxide-semiconductor (CMOS) substrate containing 65,536 recording channels, from which we can simultaneously record a selectable subset of up to 1024 channels at a given time. Fully implanted below the dura, our chip is wirelessly powered, communicating bi-directionally with an external relay station outside the body. We demonstrated chronic, reliable recordings for up to two weeks in pigs and up to two months in behaving non-human primates from somatosensory, motor, and visual cortices, decoding brain signals at high spatiotemporal resolution.

neuroscience↗

bioRxiv2024

ELONGATED HYPOCOTYL 5 (HY5) and POPEYE (PYE) Regulate Intercellular Iron Transport in Plants.

Plants maintain iron (Fe) homeostasis under varying environmental conditions by balancing processes such as Fe uptake, transport, and storage. In Arabidopsis, POPEYE (PYE), a basic helix-loop-helix (bHLH) transcription factor (TF), has been shown to play a crucial role in regulating this balance. In recent years, the mechanisms regulating Fe uptake have been well established but the upstream transcriptional regulators of Fe transport and storage are still poorly understood. In this study, we report that ELONGATED HYPOCOTYL5 (HY5), a basic leucine zipper (bZIP) TF which has recently been shown to play a crucial role in Fe homeostasis, interacts with PYE. Molecular, genetic and biochemical approaches revealed that PYE and HY5 have overlapping as well as some distinct roles in regulation of Fe deficiency response. We found that HY5 and PYE both act as a repressor of Fe transport genes such as YSL3, FRD3 NPF5.9, YSL2, NAS4, and OPT3. HY5 was found to directly bind on the promoter of these genes and regulate intercellular Fe transport. Further analysis revealed that HY5 and PYE directly interact at the same region on PYE and NAS4 promoter. Overall, this study revealed that HY5 regulates Fe homeostasis by physically interacting with PYE as well as independently.

plant biology↗

bioRxiv2024

A human papillomavirus 16 E2-TopBP1 dependent SIRT1-p300 acetylation switch regulates mitotic viral and human protein levels

An interaction between human papillomavirus 16 (HPV16) E2 and the cellular proteins TopBP1 and BRD4 is required for E2 plasmid segregation function. The E2-TopBP1 interaction promotes increased mitotic E2 protein levels in U2OS and N/Tert-1 cells, as well as in human foreskin keratinocytes immortalized by HPV16 (HFK+HPV16). SIRT1 deacetylation reduces E2 protein stability and here we demonstrate that increased E2 acetylation occurs during mitosis in a TopBP1 interacting dependent manner, promoting E2 mitotic stabilization. p300 mediates E2 acetylation and acetylation is increased due to E2 switching off SIRT1 function during mitosis in a TopBP1 interacting dependent manner, confirmed by increased p53 stability and acetylation on lysine 382, a known target for SIRT1 deacetylation. SIRT1 can complex with E2 in growing cells but is unable to do so during mitosis due to the E2-TopBP1 interaction; SIRT1 is also unable to complex with p53 in mitotic E2 wild type cells but can complex with p53 outside of mitosis. E2 lysines 111 and 112 are highly conserved residues across all E2 proteins and we demonstrate that K111 hyper-acetylation occurs during mitosis, promoting E2 interaction with Topoisomerase 1 (Top1). We also demonstrate that K112 ubiquitination promotes E2 proteasomal degradation during mitosis. The results present a model in which the E2-TopBP1 complex inactivates SIRT1 during mitosis and E2 acetylation on K111 by p300 increases, promoting interaction with Top1 that protects K112 from ubiquitination and therefore E2 proteasomal degradation. ImportanceHuman papillomaviruses are causative agents in around 5% of all human cancers. While there are prophylactic vaccines that will significantly alleviate HPV disease burden on future generations, there are currently no anti-viral strategies available for the treatment of HPV cancers. To generate such reagents, we must understand more about the HPV life cycle, and in particular about viral-host interactions. Here we describe a novel mitotic complex generated by the HPV16 E2 protein interacting with the host protein TopBP1 that controls the function of the deacetylase SIRT1. The E2-TopBP1 interaction disrupts SIRT1 function during mitosis in order to enhance acetylation and stability of viral and host proteins. This novel complex is essential for the HPV16 life cycle and represents a novel anti-viral therapeutic target.

molecular biology↗

bioRxiv2023

Algorithm for automatic detection of insulin granule exocytosis in human beta-cells

Image processing and analysis are two significant areas that are highly important for interpreting enormous amounts of data obtained from microscopy-based experiments. Several image analysis tools exist for the general detection of fundamental cellular processes, but tools to detect highly distinct cellular functions are few. One such process is exocytosis, which involves the release of vesicular content out of the cell. The size of the vesicles and the inherent differences in the imaging parameters demand specific analysis platforms for detecting exocytosis. In this direction, we have developed an image-processing algorithm based on Lagrangian particle tracking. The tool was developed to ensure that there is efficient detection of punctate structures initially developed by mathematical equations, fluorescent beads and cellular images with fluorescently labelled vesicles that can exocytose. The detection of these punctate structures using the tool was compared with other existing tools, such as find maxima in ImageJ and manual detection. The tool not only met the precision of existing solutions but also expedited the process, resulting in a more time-efficient solution. During exocytosis, there is a sudden increase in the intensity of the fluorescently labelled vesicles that look like punctate structures. The algorithm precisely locates the vesicles coordinates and quantifies the variations in their respective intensities. Subsequently, the algorithm processes and retrieves pertinent information from large datasets surpassing that of conventional methods under our evaluation, affirming its efficacy. Furthermore, the tool exhibits adaptability for the image analysis of diverse cellular processes, requiring only minimal modifications to ensure accurate detection of exocytosis.

cell biology↗

bioRxiv2023

Activin E is a TGFβ ligand that signals specifically through activin receptor-like kinase 7.

Activins are one of the three distinct subclasses within the greater Transforming Growth Factor {beta} (TGF{beta}) superfamily. First discovered for their critical roles in reproductive biology, activins have since been shown to alter cellular differentiation and proliferation. At present, members of the activin subclass include activin A (ActA), ActB, ActC, ActE, and the more distant members myostatin and GDF11. While the biological roles and signaling mechanisms of most activins class members have been well-studied, the signaling potential of ActE has remained largely unknown. Here, we characterized the signaling capacity of homodimeric ActE. Molecular modeling of the ligand:receptor complexes showed that ActC and ActE shared high similarity in both the type I and type II receptor binding epitopes. ActE signaled specifically through ALK7, utilized the canonical activin type II receptors, ActRIIA and ActRIIB, and was resistant to the extracellular antagonists follistatin and WFIKKN. In mature murine adipocytes, ActE invoked a SMAD2/3 response via ALK7, similar to ActC. Collectively, our results establish ActE as an ALK7 ligand, thereby providing a link between genetic and in vivo studies of ActE as a regulator of adipose tissue. SignificanceActivin E is a homodimeric member of the TGF{beta} family belonging to the activin subclass. Currently, the signaling capacity of ActE is unknown due to a lack of reliable reagents to study the protein. Here, we demonstrate that ActE acts as a canonical TGF{beta} ligand that signals through SMAD2/3 in an ALK7-dependent manner, similar to ActC. ActE also utilizes the activin type II receptors, ActRIIA and ActRIIB, to signal and is unable to be antagonized by FS288 and WFIKKN2. This study shows that ActE is a signaling ligand and provides a connection between genetic and in vivo studies that links ActE to adiposity.

biochemistry↗