Biology subjects

Maji, S.

Publications and source records attributed to Maji, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Ultrasound-reconfigurable scaffolds enable dynamic control of biochemical and biophysical cues for vascular network formation

Vascularization, which is critical for most engineered tissue constructs, is dependent on interactions between endothelial cells and spatiotemporally presented biochemical and biophysical cues. Yet, most hydrogels define these cues at the time of fabrication, thus precluding adjustments to actively drive vascular formation. We developed acoustically responsive scaffolds (ARSs) that use focused ultrasound to trigger growth factor release and localized matrix remodeling within fibrin hydrogels. ARSs were formed by incorporating phase-shift emulsions containing basic fibroblast growth factor (bFGF) along with perfluorohexane (C6) or perfluorooctane (C8). Upon ultrasound exposure, stable bubbles were generated in C6-ARSs that locally compacted the matrix and increased macroscale stiffness. Comparatively, in C8-ARSs, ultrasound generated macropores without impacting viscoelastic properties. Ultrasound increased bFGF release from both ARS types, which enhanced in vitro and in vivo vasculogenic assembly in ARSs with co-encapsulated endothelial cells and fibroblasts. Our data also show that ultrasound-driven matrix remodeling without bFGF release increased endothelial sprouting. In C6-ARSs, elevated levels of F-actin were observed in both cell types adjacent to bubbles as well as increased YAP intensity and nuclear asymmetry. Together, these results establish ARSs as reconfigurable hydrogels that couple on-demand release of biochemical cues with programmable matrix restructuring to direct three-dimensional microvascular assembly.

bioengineering↗

bioRxiv2026

The Dark Ecology Dataset: Measurements of Aerial Biomass in US Weather Radar from 1995 to 2025

The US NEXRAD radar network has monitored the aerosphere over the US and its territories continuously since the 1990s and archived nearly 300 million radar volume scans. These data contain a wealth of information about the movements of birds, bats, and insects. Historically, this biological information was difficult to access due to the amount of data and challenges in analyzing it. In the last 15 years, fueled by computational and methodological advances, large-scale aeroecology research has blossomed. However, comprehensive analyses of the NEXRAD archive remain very costly. We collected measurements from every volume scan in the NEXRAD archive--nearly 300 million data files total--to assemble a dataset of aerial biological activity over the US from 1995 to 2025. The core data are vertical profiles, which summarize biological activity at different heights above the radar station for each volume scan. We also provide time series data products that aggregate vertical profiles to point measurements at radar stations across time. These data products can support a range of aeroecology analyses at significantly reduced effort.

ecology↗

bioRxiv2026

Exploring the Structural and Functional role of α,β-unsaturated Ketoesters as Anti-Staphylococcal Agents Targeting Glutathione Peroxidase

Multiple-drug resistant (MDR) Staphylococcus aureus strains (like methicillin-resistant S. aureus or MRSA) uses an arsenal of antioxidant enzymes to mitigate host-induced oxidative stress. Among them the non-canonical Staphylococcal glutathione peroxidase (SaGpx) plays a crucial role in bacterial redox homeostasis by reducing peroxides via thioredoxin-dependent pathways. Thus, enabling oxidative stress mitigation during host infection. Despite its importance in S. aureus, its role in bacterial pathogenesis remains unexplored. This study aimed to elucidate the possible role of SaGpx in Staphylococcal virulence. First, we determined the high-resolution crystal structure of SaGpx (at 1.65 [A] resolution) using X-ray crystallography. Guided by the catalytic cleft architecture of SaGpx, small-molecule based inhibitors were then rationally designed and synthesized. These inhibitors exhibited good binding affinity to SaGpx and complete enzymatic blockade. These inhibitors exhibited potent anti-S. aureus activity (MICs 6.25-31.25 M) along with no cytotoxicity in L929 fibroblast wound-healing assays. Furthermore, the in vivo antibacterial ability of these inhibitors was evaluated using S. aureus-infected skin wound mouse model, where these compounds show potent antibacterial and wound healing ability supported by subsequent histological as well as immunohistochemical analysis. These findings suggest SaGpx as a possible virulence determinant in S. aureus and position these synthesized inhibitors as promising antivirulence therapeutics. HighlightsO_LIThe high-resolution crystal structure of Staphylococcal glutathione peroxidase is solved. C_LIO_LIBased on the SaGpx catalytic site, ,{beta}-unsaturated ketoesters derivatives are synthesized. C_LIO_LISynthesized ,{beta}-unsaturated ketoesters derivatives inhibit SaGpx activity and binds the protein at M range. C_LIO_LISynthesized ,{beta}-unsaturated ketoesters derivatives show in vitro antibacterial activity against S. aureus at low M range. C_LIO_LISynthesized ,{beta}-unsaturated ketoesters derivatives show in vivo antibacterial and wound healing ability S. aureus-infected skin wound mouse model. C_LI

biophysics↗

bioRxiv2026

Placentrex disrupts the biofilm formation of Pseudomonas aeruginosa through multi-target transcriptional reprogramming.

AimsPseudomonas aeruginosa biofilm-associated infections pose a significant clinical challenge due to their inherent antibiotic tolerance. This study aimed to evaluate the antibacterial and antibiofilm activity of Placentrex, a standardised aqueous placental extract, against P. aeruginosa and to elucidate its molecular mechanism of action using RNA sequencing (RNA-seq). Methods and ResultsPlacentrex exhibited potent bactericidal activity against P. aeruginosa at 50 {micro}g/mL. Biofilm formation was significantly inhibited by [~]87% at 50 {micro}g/mL after 72 hours. Preformed biofilms were eradicated by [~]93% and [~]89% at 50 and 25 {micro}g/mL, respectively. Interestingly, biofilm viability was reduced by [~]93% and [~]87% upon treatment with 50 {micro}g/mL and 25 {micro}g/mL of Placentrex, respectively. EPS characterisation revealed that the EPS contain a single large polysaccharide, and chromatography data suggested that it is made up of glucose as a monomer. RNA-seq identified coordinated downregulation of seven key genes, namely, flp major pilin (surface attachment), extracellular solute binding protein (ABC transporter-mediated nutrient sensing and biofilm maintenance), gntP permease (carbon metabolism), AraC family transcriptional regulator (quorum sensing and polysaccharide biosynthesis), ureE (urease nickel metallochaperone), aromatic amino acid permease (pyoverdine and PQS biosynthesis), and MFS transporter (efflux and autoinducer export). ConclusionsPlacentrex exerts comprehensive antibiofilm and antibacterial activity through simultaneous disruption of surface attachment, nutrient-sensing-driven biofilm maintenance, quorum sensing, carbon metabolism, urease virulence maturation, and efflux-mediated persistence. This polypharmacological mechanism supports Placentrex as a promising multi-target antibacterial agent against P. aeruginosa biofilm-associated infections. Impact statementPlacentrex is a potential anti-biofilm agent against Pseudomonas aeruginosa.

microbiology↗

bioRxiv2025

Shaping the active site from a distance: Unravelling the regulatory role of the conserved N-terminal β-flap of thiol peroxidases through structure-function characterization of the Staphylococcal ortholog

Bacterial thiol peroxidases (Tpxs) are members of atypical two-cysteine peroxiredoxin, which detoxify hydroperoxides during host-pathogen interactions. Despite extensive research on bacterial Tpxs, the precise structure-based functional characterization of Staphylococcal Tpx (SaTpx) remains elusive. Herein, we cloned and purified SaTpx along with its plausible physiological redox partners to reconstitute its electron relay system. We solved the high-resolution crystal structure of SaTpx, revealing the essential active-site catalytic triad (Cys 60, Thr 57, Arg 128). The crystal structure of SaTpx reveals the presence of the highly conserved N-terminal {beta}-flap, absent in its mammalian orthologs (Peroxiredoxin 5). To investigate the plausible role of this highly conserved {beta}-flap, we cloned and characterized a deletion mutant, N{Delta}15-SaTpx, lacking this region. N{Delta}15-SaTpx showed reduced ability to mitigate organic hydroperoxides in vitro; partially impaired to prevent ROS-mediated ds-DNA nicking and failed to protect host E. coli cells from exogenous ROS stress. The ultra-high-resolution crystal structures of N{Delta}15-SaTpx and N{Delta}15-SaTpx with substrate mimic revealed a distorted catalytic triad (with flipped Arg 128), explaining its partially impaired catalytic activity. This study, for the first time, elucidates the critical regulatory role of the N-terminal {beta}-flap in stabilizing the catalytic triad of bacterial Tpx, providing insights for future inhibitor designing. HighlightsO_LIUltra high-resolution crystal structures of SaTpx and N{Delta}15-SaTpx C_LIO_LIUltra-high resolution crystal structure of hydroperoxide substrate mimic bound N{Delta}15-SaTpx C_LIO_LI{beta}-flap deletion mediated distortion of catalytic triad in N{Delta}15-SaTpx C_LIO_LIThe novel regulatory role of the conserved N-terminal {beta}-flap of Thiol peroxidases. C_LI

biophysics↗

bioRxiv2025

Deciphering the Structure and Mechanism of SaGpx: A Non-Canonical Glutathione Peroxidase from Staphylococcus aureus

Staphylococcus aureus encounters massive oxidative stress during infection. To counter this, the bacterium developed robust antioxidative defense mechanism. Glutathione peroxidases (Gpx) are well characterized antioxidative enzymes in eukaryotes; however, their bacterial counterparts remain poorly explored. S. aureus possesses two putative Gpx genes but lacks GSH biosynthetic machinery and glutathione reductase required for canonical Gpx function, suggesting alternate electron donor system(s) may be involved. This study aimed to elucidate structure-based biochemical characterization of one of the S. aureus glutathione peroxidases homologs (SaGpx, Uniprot Id: Q2FYZ0) and identify its plausible electron donor system. Herein, we cloned, purified and determined the high-resolution crystal structure of SaGpx (1.5 [A] resolution) using X-ray diffraction crystallography. In vitro biochemical characterization of the highly conserved active site amino acid point mutants, as well as their structural disposition suggests their precise roles in the enzymes catalysis. The crystal structure of SaGpx revealed that the enzyme adopts a canonical glutathione peroxidase fold with conserved catalytic tetrad composed of C36, Q70, W124 and N125. Also, SaGpx shows similarity with mammalian Gpx4, which was previously shown to exert phospholipid hydroperoxide peroxidase activity. Furthermore, biochemical assays suggest that SaGpx utilizes Staphylococcal thioredoxin1 as its cognate electron donor. The catalytic mechanism follows an atypical 2-cysteine peroxiredoxin-like pathway involving the formation of a sulfenic acid intermediate, followed by an intramolecular disulfide bond subsequently resolved by thioredoxin. This work provides the first structure-based biochemical characterization of a bacterial glutathione peroxidase homolog, establishing the novel structural insights of SaGpx as a noncanonical thioredoxin-dependent glutathione peroxidase.

biophysics↗

bioRxiv2025

Repurposing Melatonin in dual-mode for Wilson disease therapy as a Copper Chelator and an antioxidant agent

Loss-of-function mutations in copper-ATPase ATP7B underlie Wilson disease (WD), a disorder characterized by hepatic copper accumulation and severe hepato-neuropathology. Existing chelation therapeutics remove excess copper but lack intrinsic antioxidant capacity and frequently cause systemic toxicity. Here we evaluate melatonin, an FDA-approved indoleamine with antioxidant and putative metal-chelating activity, as a candidate therapeutic for WD. In ATP7B-/- hepatocytes, melatonin restored copper-induced reactive oxygen species (ROS) to basal levels, reduced apoptosis twofold, and attenuated Nrf2 nuclear translocation leading to reduction of Hemoxygenase-1 abundance. Live-cell ratiometric analysis of GSSG/GSH using GRX1-roGFP2 expressed in melatonin-treated ATP7B-/- hepatocytes revealed a significant reduction in intensity-ratio, indicating an effective mitigation of copper-induced glutathione oxidation. Isothermal calorimetric titration revealed moderate Cu2+ affinity (K ITC=4.54 x 103 M-{superscript 1}), rationalized by MD-simulations showing an interaction energy of 18.5 x 10-3 kcal{middle dot}mol-{superscript 1} via amide-Cu{superscript 2} coordination. In-cellulo studies also revealed that copper-induced vesicularized ATP7B reinstates to Golgi in melatonin-treated hepatocytes. In vivo, melatonin treatment reduced copper-induced oxidative stress in zebrafish embryos and lowered copper burden in Caenorhabditis elegans WD model. Our studies revealed that encapsulation of melatonin within an engineered polymeric nanocapsules having dithiol linkers, susceptible to cleavage by GSH, extended melatonins circulatory half-life ten-fold and enhanced its ROS-scavenging efficacy three-fold relative to free melatonin. This work introduces a unique dual-function therapeutic strategy that integrates antioxidant activity with copper chelation, simultaneously addressing copper overload and redox imbalance. Repurposing melatonin, with its established clinical safety, offers rapid and cost-effective translational pathway toward WD-therapy while providing a generalizable platform for redox- and metal-associated disorders.

cell biology↗

bioRxiv2025

Structures of Naked Mole-Rat, Tuco-Tuco, and Guinea Pig Ribosomes: Is rRNA Fragmentation Linked to Translational Fidelity?

Ribosomes are central to protein synthesis in all organisms. Among mammals, the ribosome functional core is highly conserved. Remarkably, two rodent species, the naked mole-rat (NMR) and tuco-tuco display fragmented 28S rRNA, coupled with high translational fidelity and long lifespan. The unusual ribosomal architecture in the NMR and tuco-tuco has been speculated to be linked to high translational fidelity. Here we show, by single-particle cryo-electron microscopy (cryo-EM), that despite the fragmentation of their rRNA, NMR and tuco-tuco ribosomes retain their core functional architecture. Compared to ribosomes of the guinea pig, a phylogenetically related rodent without 28S rRNA fragmentation, ribosomes of NMR and tuco-tuco exhibit poorly resolved, certain expansion segments. In contrast, the structure of the guinea pig ribosome shows high similarity to human ribosome. Enhanced translational fidelity in the NMR and tuco-tuco may stem from subtle, allosteric effects in dynamics, linked to rRNA fragmentation.

biochemistry↗

bioRxiv2025

Coronavirus protein interaction mapping in bat and human cells identifies molecular and genetic switches for immune evasion and replication

Coronaviruses, including SARS-CoV-2, can cause severe disease in humans, whereas reservoir hosts like Rhinolophus bats remain asymptomatic. To investigate how host-specific protein-protein interactions (PPIs) influence infection, we generated comparative PPI maps for SARS-CoV-2 and its bat-origin relative RaTG13 using affinity purification-mass spectrometry (AP-MS) in human and Rhinolophus ferrumequinum (RFe) bat cells. This approach identified both conserved and virus- and host-specific interactions that regulate infection dynamics. Notably, SARS-CoV-2 required a non-synonymous mutation in nucleocapsid to replicate in bat cells expressing human ACE2 and TMPRSS2. Analysis of the viral protein Orf9b revealed differential interactions with mitochondrial proteins Tom70 and MTARC2. A single residue difference in Orf9b between SARS-CoV-2 and RaTG13 functions as a molecular switch, weakening Tom70 binding and immune evasion in human cells while enhancing interaction with the bat-specific restriction factor MTARC2. These findings demonstrate how a single-residue substitution can reshape virus-host interactions and contribute to immune evasion and host adaptation.

systems biology↗

bioRxiv2025

Conserved inter-domain interactions drive trans-Golgi network localisation and trafficking of homologous copper-ATPases

Polytopic transmembrane Copper-ATPases are central regulators of the essential, redox-active micronutrient copper in all organisms. The vertebrate Cu-ATPase homologs ATP7A and ATP7B facilitate excess copper efflux, in addition to metalating cuproproteins. ATP7A and ATP7B exhibit copper-responsive basolateral and apical trafficking polarity respectively, in polarized epithelia. To elucidate the role of conserved functional domains in copper-responsive trafficking and copper transport, we substituted the copper-binding amino-terminal, Nucleotide-Binding (NBD) and C-terminal domain of ATP7B with that of ATP7A either singly or in combinations. The six chimeric Cu-ATPases generated, although functionally active, exhibited altered trafficking phenotypes. Notably, the N-terminal-substituted ATP7B exhibited constitutive trafficking to the basolateral membrane; however, the N-terminal and NBD double-substituted chimera gained steady-state TGN localization, indicating a putative interaction between the two domains critical for its TGN-localization. We analyzed orthologous Cu-ATPase domain sequences from diverse organisms and found that the N-terminal domain and NBD showed similar evolutionary relationships, unlike that of C-terminal domain, suggesting their co-evolution. This study for the first time correlates evolutionary stringency imparted onto Cu-ATPase domains with their significance in proper trafficking regulation.

cell biology↗

bioRxiv2025

Non-canonical regulation of the plasma membrane copper transporter CTR1 through modulation of membrane mechanical properties

We describe a non-canonical, membrane receptor-like regulation of the human copper transporter CTR1 in response to copper stimuli. CTR1 is the sole high-affinity trimeric plasma-membrane copper-importing channel that self-regulates by undergoing endocytosis to limit copper uptake. We observed that preceding copper-induced endocytosis, CTR1 forms clusters on the plasma membrane, a phenomenon that is typically observed in membrane receptors. We deciphered the mechanism of CTR1 clustering and studied its ramifications on plasma membrane physical properties harboring the clusters that favors endocytosis. Membrane tension and fluctuation are fundamental regulators of pre- and post-endocytic events. Using coarse-grain MD simulation and coupled Interference Reflection Microscopy-Total Internal Reflection Fluorescence Microscopy we demonstrated that CTR1 clusters induce positive membrane curvature, increase in local membrane tension and decrease in local membrane fluctuation; alterations that favors formation of endocytic pits. Clustering is facilitated by copper-sequestering Methionine rich extracellular amino-terminus of CTR1. MD-simulations and IRM-TIRF imaging revealed that CTR1 clustering is facilitated by membrane cholesterol, depletion of which delays CTR1 endocytosis. CTR1 clustering promotes clathrin-coated pit formation that engages recruitment of adapter protein AP-2. To summarize, we report a hitherto unknown pre-endocytic receptor-like phenomenon of ligand-induced clustering of a metal channel, that in-turn regulates self-endocytosis by modulating membrane properties.

cell biology↗

bioRxiv2025

Ku suppresses RNA-mediated innate immune responses in human cells to accommodate primate-specific Alu expansion.

Ku70 and Ku80 form Ku, a ring-shaped protein that initiates the non-homologous end-joining (NHEJ) DNA repair pathway.1 Specifically, Ku binds to double-stranded DNA (dsDNA) ends and recruits other NHEJ factors (e.g., DNA-PKcs and LIG4). While Ku binds to double-stranded RNA (dsRNA)2 and traps mutated-DNA-PKcs on ribosomal RNA in vivo,3,4 the physiological significance of Ku-dsRNA interactions in otherwise wild-type cells remains elusive. Intriguingly, while dispensable for murine development,5,6 Ku is essential in human cells.7 Despite similar genome sizes, human cells express [~]100-fold more Ku than mouse cells, implying functions beyond NHEJ, possibly through a dose-sensitive interaction with dsRNA, which is [~]100 times weaker than with dsDNA.2,8 While investigating the essentiality of Ku in human cells, we found that depletion of Ku - unlike LIG4 - induces profound interferon (IFN) and NF-kB responses reliant on the dsRNA-sensor MDA5/RIG-I and adaptor MAVS. Prolonged Ku-degradation also activates other dsRNA-sensors, e.g. PKR that suppresses protein translation, and OAS/RNaseL that cleaves rRNAs and eventually induces growth arrest and cell death. MAVS, RIG-I, or MDA5 knockouts suppressed IFN signaling and, together with PKR knockouts, partially rescued Ku-depleted human cells. Ku-irCLIP analyses revealed that Ku binds to diverse dsRNA, predominantly stem-loops in primate-specific Alu elements9 at anti-sense orientation in introns and 3-UTRs. Ku expression rose sharply in higher primates tightly correlating with Alu-expansion (r = 0.94/0.95). Together, our study identified a vital role of Ku in accommodating Alu-expansion in primates by mitigating a dsRNA-induced innate immune response, explaining the rise of Ku levels and its essentiality in human cells.

genetics↗

bioRxiv2024

AcrIF11 is a potent CRISPR-specific ADP-ribosyltransferase encoded by phage and plasmid

Phage-encoded anti-CRISPR (Acr) proteins inhibit CRISPR-Cas systems to allow phage replication and lysogeny maintenance. Most of the Acrs characterized to date are stable stoichiometric inhibitors. While enzymatic Acrs have been characterized biochemically, little is known about their potency, specificity, and reversibility. Here, we examine AcrIF11, a widespread phage and plasmid-encoded ADP-ribosyltransferase (ART) that inhibits the Type I-F CRISPR-Cas system. We present an NMR structure of an AcrIF11 homolog that reveals chemical shift perturbations consistent with NAD (cofactor) binding. In experiments that model both lytic phage replication and MGE/lysogen stability under high targeting pressure, AcrIF11 is a highly potent CRISPR-Cas inhibitor and more robust to Cas protein level fluctuations than stoichiometric inhibitors. Furthermore, we demonstrate that AcrIF11 is remarkably specific, predominantly ADP-ribosylating Csy1 when expressed in P. aeruginosa. Given the reversible nature of ADP-ribosylation, we hypothesized that ADPr eraser enzymes (macrodomains) could remove ADPr from Csy1, a potential limitation of PTM-based CRISPR inhibition. We demonstrate that diverse macrodomains can indeed remove the modification from Csy1 in P. aeruginosa lysate. Together, these experiments connect the in vitro observations of AcrIF11s enzymatic activity to its potent and specific effects in vivo, clarifying the advantages and drawbacks of enzymatic Acrs in the evolutionary arms race between phages and bacteria.

microbiology↗

bioRxiv2024

KDM6A Regulates Immune Response Genes in Multiple Myeloma

The histone H3K27 demethylase KDM6A is a tumor suppressor in multiple cancers, including multiple myeloma (MM). We created isogenic MM cells disrupted for KDM6A and tagged the endogenous protein to facilitate genome wide studies. KDM6A binds genes associated with immune recognition and cytokine signaling. Most importantly, KDM6A binds and activates NLRC5 and CIITA encoding regulators of Major Histocompatibility Complex (MHC) genes. Patient data indicate that NLRC5 and CIITA, are downregulated in MM with low KDM6A expression. Chromatin analysis shows that KDM6A binds poised and active enhancers and KDM6A loss led to decreased H3K27ac at enhancers, increased H3K27me3 levels in body of genes bound by KDM6A and decreased gene expression. Reestablishing histone acetylation with an HDAC3 inhibitor leads to upregulation of MHC expression, offering a strategy to restore immunogenicity of KDM6A deficient tumors. Loss of Kdm6a in murine RAS-transformed fibroblasts led to increased growth in vivo associated with decreased T cell infiltration. Statement of significanceWe show that KDM6A participates in immune recognition of myeloma tumor cells by directly regulating the expression of the master regulators of MHC-I and II, NLRC5 and CIITA. The expression of these regulators can by rescued by the HDAC3 inhibitors in KDM6A-null cell lines.

cancer biology↗

bioRxiv2023

Leishmania major-induced alteration of host cellular and systemic copper homeostasis drives the fate of infection

Copper plays a key role in host-pathogen interaction. We found that during Leishmania major infection, the parasite-harboring macrophage regulates its copper homeostasis pathway in a way to facilitate copper-mediated neutralization of the pathogen. Copper-ATPase ATP7A transports copper to amastigote-harboring phagolysosomes to induce stress on parasites. Leishmania in order to evade the copper stress, utilizes a variety of manipulative measures to lower the host-induced copper stress. It induces deglycosylation and degradation of host-ATP7A and downregulation of copper importer, CTR1 by cysteine oxidation. Additionally, Leishmania induces CTR1 endocytosis that arrests copper uptake. In mouse model of infection, we report an increase in systemic bioavailable copper in infected animals. Heart acts as the major organ for diverting its copper reserves to systemic circulation to fight-off infection by downregulating its CTR1. Our study explores reciprocal mechanism of manipulation of host copper homeostasis pathway by macrophage and Leishmania to gain respective advantages in host-pathogen interaction.

cell biology↗

bioRxiv2023

Regulation of apico-basolateral trafficking polarity of homologous Copper-ATPases ATP7A and ATP7B

We suggest a model of apico-basolateral sorting in polarized epithelia using homologous Cu-ATPases as membrane cargoes. In polarized epithelia, upon copper treatment, homologous copper-ATPases ATP7A and ATP7B traffic from trans-Golgi network (TGN) to basolateral and apical membranes respectively. We characterized sorting pathways of Cu-ATPases between TGN and plasma-membrane and identified the machinery involved. ATP7A and ATP7B reside on distinct domains of TGN and in high copper, ATP7A traffics directly to basolateral membrane, whereas ATP7B traverses common-recycling, apical-sorting and apical-recycling endosomes en-route to apical membrane. Mass-spectrometry identified regulatory partners of ATP7A and ATP7B that include Adaptor Protein-1 complex. Upon knocking-out pan-AP-1, sorting of both copper-ATPases are disrupted. ATP7A loses polarity and localizes on both apical and basolateral surfaces in high copper. Contrastingly, ATP7B loses TGN-retention but retains apical polarity that becomes copper-independent. Using isoform-specific knockouts, we found that AP-1A provides directionality and TGN-retention for both Cu-ATPases, whereas, AP-1B governs polarized trafficking of ATP7B solely. Trafficking phenotypes of Wilson disease-causing ATP7B mutants that disrupts putative ATP7B-AP1 interaction further substantiates the role of AP-1 in apical sorting of ATP7B. Summary statementThe Adapter Protein-1 (AP-1) isoforms AP-1A and AP-1B governs the apico-basolateral trafficking polarities of the homologous Copper-ATPases, ATP7A and ATP7B at the trans-Golgi network.

cell biology↗

bioRxiv2022

Copper-independent lysosomal localization of the Wilson disease protein ATP7B

In hepatocytes, the Wilson disease protein ATP7B resides on trans-Golgi network and traffics to peripheral lysosomes to export excess intracellular copper through lysosomal exocytosis. We found that in basal copper or even upon copper chelation, a significant amount of ATP7B persists in endolysosomal compartment of hepatocytes but not in non-hepatic cells. These ATP7B-harboring lysosomes lie in close proximity of [~]10nm to the TGN. ATP7B constitutively distributes itself between the sub-domain of the TGN with a lower pH and the TGN-proximal lysosomal compartments. Presence of ATP7B on TGN-Lysosome colocalizing sites upon Golgi disruption suggested possible exchange of ATP7B directly between the TGN and its proximal lysosomes. Manipulating lysosomal positioning significantly alters the localization of ATP7B in the cell. Contrary to previous understanding, we found that upon copper chelation in a copper-replete hepatocyte, ATP7B is not retrieved back to TGN from peripheral lysosomes; rather, ATP7B recycles to these TGN-proximal lysosomes to initiate the next cycle of copper transport. We report a hitherto unknown copper-independent lysosomal localization of ATP7B and the importance of TGN-proximal lysosomes but not TGN as the terminal acceptor organelle of ATP7B in its retrograde pathway. SynopsisExcess copper is toxic to the cell. In hepatocytes, the Wilson disease protein ATP7B has been reported to recycle between the trans-Golgi network and lysosomes to export copper in elevated copper conditions. We, for the first time, show that a large fraction of ATP7B constitutively resides on the lysosome and rather, the position of the lysosome shifts from TGN-proximal to the peripheral region of the cell in high copper to facilitate ATP7B-mediated lysosomal exocytosis of copper.

cell biology↗

bioRxiv2022

Using spatio-temporal information in weather radar data to detect and track communal bird roosts

O_LIThe exodus of swallows from communal nighttime roosts is often visible as an expanding ring-shaped pattern in weather radar data. The WSR-88D network operated by the National Weather Service archives more than 25 years of data across 143 stations in the contiguous US. However, access to information about the roosting behavior of swallows is limited by the cost of manual annotation of these scans. C_LIO_LIWe develop an AI system to detect and track swallow roosts in weather radar data. Our model is based on the Faster R-CNN architecture and is customized to incorporate multiple spatial and temporal channels in volumetric radar scans using novel adaptor layers. We systematically study the impact of network architecture and input representation for this task. We incorporate our detection outputs into an AI-assisted system with an interface for human screening to collect research-grade data about roosting behavior. We deploy the system to collect information from 12 radar stations in the Great Lakes region of the US spanning 21 years. C_LIO_LIThe addition of temporal information improves roost detection performance from 47.0% mean average precision to 54.7%. Temporal information helps the model recognize the expanding pattern of roosts and filter false positives due to rain and static structures. Our system allowed the annotation of 15,628 roost signatures with 64,620 single-frame detections in 612,786 radar scans with 183.6 total hours of human screening, or 1.08 seconds per radar scan. C_LIO_LIOur AI-assisted system provides research-quality roost data with far less human effort than manual annotation of radar scans. The data contains critical information about the phenology and population trends of swallows and martins, a declining group of aerial insectivores. Our successful deployment to collect historical data for 8% of the radar stations in the contiguous US lays the groundwork for continentscale analysis of swallow roosts, and provides a starting point for analysis of other family-specific phenomena in weather radar, such as bat roosts and mayfly hatches. C_LI

ecology↗