Biology subjects

Johnston, J.

Publications and source records attributed to Johnston, J..

At least 19 recordsLinked to original sources

bioRxiv2026

BI-TfR1 CapX rapidly transits the blood-brain barrier for efficient, low-dose gene delivery throughout the CNS

Safe, efficient gene delivery throughout the CNS remains a central obstacle to treating genetic diseases of the brain and spinal cord. We describe BI-TfR1 CapX, a human transferrin receptor (TfR1)-binding AAV capsid that, after a low intravenous dose in adult humanized TFRC mice, transduced more than 80% of cortical and spinal neurons and ~60% of cortical astrocytes, with reduced distribution and expression in several peripheral tissues relative to AAV9. Unlike other engineered BBB-crossing capsids, CapX bound the CNS vasculature within minutes and a large fraction of its genomes reached parenchymal nuclei within 24 hours. Delivering a Prnp-targeted epigenetic silencer (Prnp-CHARM), CapX reduced brain Prnp mRNA by over 95% requiring 18-fold fewer vector genomes per brain cell than AAV-PHP.eB for 50% lowering. A CapX delivered dual-vector cytosine base editor installed a protein-truncating PRNP stop codon lowering brain prion protein by 80%. These properties make CapX an attractive vehicle for human CNS gene therapy.

neuroscience↗

bioRxiv2026

Genome-resolved and kinetic evidence for low-DO comammox-anammox synergy and acetate-stimulated nitrate reduction in IFAS biofilms

Mainstream anammox implementation for nitrogen removal is constrained by unstable nitrite supply and organic carbon requirements for nitrate byproduct removal. This study evaluated integrated fixed-film activated sludge (IFAS) biofilms to enhance anammox activity by coupling low-oxygen ammonium oxidation with volatile fatty acid (VFA)-driven nitrate reduction. Nanopore long-read metagenomic assembly recovered a high-quality, circular single-contig Candidatus Brocadia sapporoensis metagenome-assembled genome (MAG) from full-scale IFAS biofilms. This MAG encodes complete anammox metabolism, dissimilatory nitrate reduction to ammonium (DNRA) and acetate/propionate carbon transformation pathways. Metatranscriptomics showed that low dissolved oxygen (DO) upregulated Ca. B. sapporoensis genes involved in anammox, nitrate reduction, and carbon metabolism. Microaerobic assays established a DO level of 0.7 mg/L as optimal for sustaining near-maximal ammonium oxidation alongside anammox-driven total inorganic nitrogen (TIN) loss. Anoxic tests conducted in secondary effluent indicated that external acetate amendment promoted greater partial nitrate reduction and TIN loss than additional propionate amendment. Integrating this dissolved oxygen concentration with external acetate amendment in a two-stage microaerobic-anoxic system successfully achieved sequential ammonium oxidation, partial nitrate reduction, and anammox-mediated TIN removal. Stage-specific expression suggested Ca. B. sapporoensis could contribute to nitrite self-supplementation via nxrAB-mediated nitrate reduction. Overall, microaerobic ammonium oxidation and Ca. B. sapporoensis-driven partial nitrate reduction jointly sustain mainstream anammox activity. Furthermore, this study demonstrates that successful metabolic synergy depends fundamentally upon precise dissolved oxygen control and effective external acetate amendment.

microbiology↗

bioRxiv2026

Insulin controls olfactory gain at the first central synapse by regulating periglomerular neuron excitability

Sensory processing is dynamically tuned by internal state, yet how metabolic signals reshape the earliest stages of sensory circuits remains poorly understood. Here we identify a circuit mechanism by which satiety suppresses olfactory sensitivity at the first central synapse in the mouse olfactory bulb. Using a within-animal paradigm modelling fasted and glucose-induced sated states, we show that satiety impairs food-finding behaviour and reduces olfactory receptor neuron input to the olfactory bulb. Periglomerular (PG) cells, which co-express insulin receptors and the potassium channel Kv1.3, mediate this effect: insulin inhibits the low-voltage-activated Kv1.3 current in PG cells, increasing their spontaneous and odour-evoked activity. This heightened PG cell activity drives enhanced presynaptic inhibition of olfactory receptor neuron terminals, dampening sensory input before it reaches mitral cells. These findings establish insulin-dependent presynaptic inhibition of PG cells as a key locus of state-dependent sensory gain control.

neuroscience↗

bioRxiv2026

Music-Inspired Acoustic-Piezoelectric Stimulation Accelerates Extracellular Vesicle Production and Programs Therapeutic Function

Macrophage small extracellular vesicles (sEVs) carry phenotype-linked cargo and bioactivity for immunomodulation and regeneration, but therapeutic translation is limited by low secretion and poor control of function. We introduce a music-activated piezoelectric nanofiber substrate (PES) that converted audible sound into programmable electrical stimulation to enhance sEV biogenesis while tuning macrophage polarization. Adjusting acoustic parameters increased sEV yield, while musically inspired "assemblies" biased macrophage phenotypes: dissonant, low-frequency stimuli promoted M1-like inflammation, whereas consonant, higher-frequency stimuli favored M2-like, regenerative states. These shifts produced distinct sEV cargo and bioactivities. We rationally designed customized music stimulus that maximized both vesicle production and M2 bias, yielding sEVs exhibited regeneration potentials. This work establishes a programmable acoustic-piezoelectric strategy to scale macrophage sEV production while tailoring their therapeutic potency.

bioengineering↗

bioRxiv2025

Image-Based Profiling of Induced Trophoblast Stem Cells Identifies Signatures Associated with Sex, Schizophrenia Genomic Risk and Placental Stress

Schizophrenia (SCZ) is a neurodevelopmental disorder where both genetic and environmental risks converge during pregnancy. Recent studies have highlighted the importance of placental biology in influencing risk of developing SCZ. However, the pathways by which genetic risk factors for SCZ interact with environmental influences to alter placental development are poorly understood. Through image-based profiling using Cell Painting, we leveraged trophoblast cultures derived from human induced pluripotent stem cells (hiPSCs) from male and female SCZ and neurotypical donors with varying placental genomic risk scores (PlacGRS) to explore the developmental dynamics of placental cells under normal growth and hypoxic stress. We employed both classical (e.g., CellProfiler) and deep learning feature extraction combined with downstream supervised machine learning to analyze high-dimensional data obtained from this hiPSC-derived model system, highlighting that these approaches overcome the inherent line-to-line variability in phenotypic analysis. Our findings reveal a salient nucleus-localized SCZ risk signature across cell lines, along with clear sexual dimorphism. This research underscores the capability of hiPSC-derived placenta models to elucidate complex interactions between genetic risk and environmental factors implicated in the neurodevelopment of SCZ, paving the way for future studies aimed at developing targeted therapeutic and prevention strategies.

neuroscience↗

bioRxiv2025

Hot and Bothered, Bees Gut Microbiome Shifts Under Thermal Stress and Pathogen Infection.

Understanding bumble bee gut health is imperative as these vital pollinators are subjected to pathogenic infections and thermal stress from climate change. The gut microbiome serves as an indicator for health and fitness and indicates the types of stress. To investigate the combined effects of thermal stress and pathogenic infection on bee guts, we performed a two-by-two crossed design where Bombus impatiens workers were subjected to hot conditions, pathogenic infection, or both. Incubation groups were given 2-weeks of stress conditions, with infected bees initially inoculated with Crithidia bombi, a common bee gut parasite. We measured body size, quantified the infection intensity of C. bombi using qPCR, and defined the composition of the gut microbiome using full-length 16S rRNA gene amplicon sequencing on an Oxford Nanopore Technologies Mk1D. While the core gut microbiome thrived with genera such as Bombilactobacillus and Snodgrassila which were not impacted by treatment; there were notable changes in other key organisms. Asaia bogorensis spiked in control temperature infected organisms, while species of Lactobacillus were overtaken in hot temperatures by significant increases in Apilactobacillus kunkeei. Species such as Citrobacter freundii dominated in hot infected bees suggesting an increased immunocompromised state from the combined stressors impacts on bee gut health. Our novel combined effects from thermal stress and pathogenic infection strengthen existing literature and provide new directions on how to quantify the health-state of wild bees based on their gut microbiome composition. These insights enable us to better understand how bees will be further impacted in changing landscapes. ImportanceWe find significant changes in bees gut microbiome especially with an increased abundance of lactic acid bacteria. These lactic acid bacteria are often specialized: based on infection status, temperature, and the combined effects. These insights are vital to researchers, especially those studying wild bee gut health where they have an uncontrolled system and need to make assumptions about bee stress based on fitness and microbiome. Our detailed outline of relevant species will provide wild bee researchers with a baseline to determine thermal stress and recent infection status based on microbiome communities. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/687019v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1528ae6org.highwire.dtl.DTLVardef@1d100dorg.highwire.dtl.DTLVardef@8ea77org.highwire.dtl.DTLVardef@159620a_HPS_FORMAT_FIGEXP M_FIG C_FIG Overview of the experimental design where bees were either given control temperatures or thermal stress and/or an infection by Crithidia bombi. The bees microcolonies were incubated for 2-weeks before sacrificing the bees, extracting DNA, and performing downstream analysis. Full length 16S rRNA gene amplicon sequencing was performed on an Oxford Nanopore MK1D sequencer while Crithidia bombi infections were quantified using quantitative polymerase chain reaction.

ecology↗

bioRxiv2025

M1 Macrophage-Derived Small Extracellular Vesicles as Synergistic Nanotherapeutics: Harnessing Intrinsic Anticancer Activity and Drug Delivery Capacity

Small extracellular vesicles (sEVs) have emerged as next-generation multifunctional nanotherapeutics due to their parental-cell traits and role in intercellular communication. Among them, immune cell-derived sEVs are uniquely positioned to couple innate immunomodulatory activities with therapeutic payload delivery, making them highly attractive for cancer therapy. In particular, M1 macrophage-derived sEVs (M1-sEVs) preserve the tumor-suppressive functions of their parent cells, including tumor microenvironment (TME) reprogramming, immune activation, and inhibition of cancer progression. However, the mechanisms by which these activities are coordinated within the TME, and whether they act independently or synergistically, remain poorly understood. Clarifying these mechanisms is crucial for harnessing their intrinsic bioactivity in combination with their natural capacity as drug delivery nanocarriers to optimize therapeutic efficacy. Here, we demonstrate that M1-sEVs exhibit intrinsic stability and circulation longevity via do not eat me ligands, as well as tumor-homing ability revealed by proteomic profiling, enabling efficient uptake and deep infiltration in breast cancer models. Functionally, M1-sEVs deliver antiproliferative microRNAs that suppress tumor metabolism, growth, and progression by inhibiting self-renewal, adhesion, migration, motility, and invasion. Importantly, by integrating this endogenous bioactivity with exogenous doxorubicin loading, we achieved synergistic efficacy: a 3-fold reduction in IC50 in vitro (0.46 M vs. 1.45 M for free drug) and 70.18% tumor growth inhibition in vivo. These findings highlight M1-sEVs as dual-action nanotherapeutics that combine innate immune-regulatory and tumor-inhibitory functions with efficient drug delivery, advancing their development as powerful platforms for cancer therapy.

bioengineering↗

bioRxiv2025

Screening of a kinase library in human Huntington disease iPSC derived striatal precursor neurons reveals a neuroprotective effect of PKC alpha and PKC beta1 inhibition

The loss of striatal medium spiny neurons is a hallmark of Huntingtons disease (HD). To identify potential disease-modifying treatments, we previously developed a human neuronal model by immortalizing and differentiating HD patient-derived iPSCs into highly homogeneous striatal precursor neurons (ISPNs). Using a 96-well screening platform, and two rounds of re-screening, we tested a kinase inhibitor library and identified 5 compounds that protected HD ISPNs from mutant huntingtin (mHTT)-induced toxicity. Among these, we prioritized the PKC-/{beta}1 inhibitor GO6976, which rescued HD ISPNs from mHTT toxicity in a dose-dependent manner. Further, we found increased phosphorylation of PKC- and PKC-{beta}1 in HD cells and tissues, while their overexpression was toxic to HD ISPNs. Knockdown of PKC-/{beta}1 protected the neurons, and both isoforms interacted and colocalized with HTT. These results suggest that PKC-/{beta}1 plays a role in HD neurodegeneration, and that inhibiting their activity may offer a potential therapeutic approach for HD. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=194 SRC="FIGDIR/small/677178v2_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@256d6org.highwire.dtl.DTLVardef@1931e7borg.highwire.dtl.DTLVardef@1b6598borg.highwire.dtl.DTLVardef@b0bbb5_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIHD patient-derived iPSC-based striatal precursor neurons (ISPNs) were used to screen and identify neuroprotective compounds. C_LIO_LIThe PKC-/{beta}1 inhibitor GO6976 rescues HD ISPNs from mutant huntingtin (HTT)-induced toxicity. C_LIO_LIThe phosphorylation of PKC-/{beta}1 is elevated in HD cell and tissues, and PKC-/{beta}1 interact with both wild-type and mutant huntingtin. C_LIO_LIOverexpression of PKC-/{beta}1 is toxic to HD ISPNs, while its knockdown protects the neurons. C_LI

neuroscience↗

bioRxiv2025

Additive effects on craniofacial development upon conditional ablation of PDGFRα and SHP2 in the mouse neural crest lineage

BackgroundActivity of the receptor tyrosine kinase PDGFR and the tyrosine phosphatase SHP2 are critical for vertebrate craniofacial development. We sought to determine the effect of SHP2 binding to PDGFR via phenotypic and biochemical analyses of an allelic series of mouse embryos with combined loss of both proteins in the neural crest lineage. ResultsWe demonstrated that SHP2 preferentially binds PDGFR/ homodimers among the three PDGFR dimers. Analysis of allelic series mutant embryos revealed increased cell death in the lateral nasal and maxillary processes at E10.5, variably penetrant facial blebbing, facial hemorrhaging, midline clefting and loss of the mandibular region at E13.5, and widespread craniofacial bone and cartilage defects at birth. Further, we showed that loss of SHP2 leads to increased phosphorylation of PDGFR and the downstream effector Erk1/2 in E10.5 allelic series mutant embryo lysates. ConclusionsTogether, our findings demonstrate additive effects on craniofacial development upon conditional ablation of PDGFR and SHP2 in the mouse neural crest lineage and indicate that SHP2 may negatively and positively regulate PDGFR signaling through distinct mechanisms.

developmental biology↗

bioRxiv2025

Transgenic A53T mice have astrocytic α-synuclein aggregates in dopamine and striatal regions

AimsParkinsons disease is considered biologically a neuronal -synuclein disease, largely ignoring the more widespread -synuclein deposition that occurs in astrocytes, with the aim of this study to identify whether astrocytes accumulate small -synuclein aggregates before or after neurons. MethodsFixed serial midbrain and striatal sections from M83 A53T transgenic mouse model of Parkinsons disease and wild-type controls were histologically processed for multiplex labelling of -synuclein and astrocytic markers and astrocyte quantitation performed on digital images using QuPath software. ResultsThe density of astrocytes within the substantia nigra pars compacta was approximately 30% greater compared with other sampled regions (P<0.005). Small aggregates of -synuclein were observed in astrocytic processes, including in wild-type mice where a quarter of all astrocytes had an obvious -synuclein aggregate. Compared to wild-type, A53T transgenic astrocytes had significantly enlarged somas (P<0.001) with more processes (P<0.001) consistent with a reactive phenotype. The A53T transgenic mice had more than double the numbers of astrocytes (P<0.001) and 2.5 times more astrocytes with -synuclein aggregates compared to wild-type mice (P<0.001). ConclusionsThese data suggest that small -synuclein aggregates are normally cleared by astrocytes and that the substantia nigra pars compacta requires more astrocytic support for this function than other midbrain dopaminergic regions or the striatum. This adds another vulnerability factor to those already known for the substantia nigra with early deficits in clearance of small -synuclein aggregates by astrocytes associated with an increased astrocytic reactivity in the A53T transgenic mouse model. Key PointsO_LIThe substantia nigra pars compacta contains a higher density of astrocytes than the ventral tegmental area or striatum, indicating a greater reliance on astrocytic function and a greater vulnerability to astrocyte dysfunction C_LIO_LISmall aggregates of -synuclein were observed in wild-type midbrain and striatal astrocytes, indicating normal clearance of -synuclein by these astrocytes C_LIO_LIMidbrain and striatal astrocytes from A53T transgenic astrocytes have more than double the number of astrocytes and more astrocytes containing -synuclein aggregates which have a reactive morphological phenotype. C_LI

neuroscience↗

bioRxiv2024

Accurate and fast segmentation of filaments and membranes in micrographs and tomograms with TARDIS

Segmentation of macromolecular structures is the primary bottleneck for studying biomolecules and their organization with electron microscopy in 2D/3D - requiring months of manual effort. Transformer-based Rapid Dimensionless Instance Segmentation (TARDIS) is a deep learning framework that automatically and accurately annotates membranes and filaments. Pre-trained TARDIS models can segment electron tomography (ET) reconstructions from both 3D and 2D electron micrographs of cryo and plastic-embedded samples. Furthermore, by implementing a novel geometric transformer architecture, TARDIS is the only method to provide accurate instance segmentations of these structures. Reducing the annotation time for ET data from months to minutes, we demonstrate segmentation of membranes and filaments in over 13,000 tomograms in the CZII Data Portal. TARDIS thus enables quantitative biophysical analysis at scale for the first time. We show this in application to kinetochore-microtubule attachment and viral-membrane interactions. TARDIS can be extended to new biomolecules and applications and open-source at https://github.com/SMLC-NYSBC/TARDIS.

bioinformatics↗

bioRxiv2024

Insulin evokes release of endozepines from astrocytes of the NTS to modulate glucose metabolism

The central nervous system (CNS) plays a key role in regulating metabolic functions, but conditions like obesity and diabetes can disrupt this balance. Within the CNS, the nucleus of the solitary tract (NTS) in the dorsal vagal complex (DVC) controls glucose metabolism and feeding behaviour. In rodents, the NTS senses insulin and communicates with the liver to regulate glucose production. Even short-term exposure to a high-fat diet (HFD) can lead to insulin resistance and impair NTS function. However, we still know little about which cells in the NTS are sensitive to insulin. Our study aimed to identify these insulin-sensitive cells and understand how they affect glucose metabolism. We found that insulin receptors in astrocytes are crucial for the NTSs ability to regulate glucose production in the liver. Insulin evokes the release of endozepines from astrocytes, and injecting endozepines into the NTS reduces glucose production. The effect of endozepines within the NTS is mimicked by GABAA antagonists and prevented by an agonist, suggesting that insulin prompts astrocytes to release endozepines, which then attenuate GABAA receptor activity, ultimately reducing glucose production in the liver. Our study is the first to show that insulin-dependent release of endozepines from NTS- astrocytes is fundamental to control blood glucose levels, providing valuable insights into the mechanisms underlying insulin function within this specific region of the CNS.

neuroscience↗

bioRxiv2024

Stimulative piezoelectric nanofibrous scaffolds for enhanced small extracellular vesicle production in 3D cultures

Small extracellular vesicles (sEVs) have great promise as effective carriers for drug delivery. However, the challenges associated with the efficient production of sEVs hinder their clinical applications. Herein, we report a stimulative 3D culture platform for enhanced sEV production. The proposed platform consists of a piezoelectric nanofibrous scaffold (PES) coupled with acoustic stimulation to enhance sEV production of cells in a 3D biomimetic microenvironment. Combining cell stimulation with a 3D culture platform in this stimulative PES enables a 15.7-fold increase in the production rate per cell with minimal deviations in particle size and protein composition compared with standard 2D cultures. We find that the enhanced sEV production is attributable to the activation and upregulation of crucial sEV production steps through the synergistic effect of stimulation and the 3D microenvironment. Moreover, changes in cell morphology lead to cytoskeleton redistribution through cell-matrix interactions in the 3D cultures. This in turn facilitates intracellular EV trafficking, which impacts the production rate. Overall, our work provides a promising 3D cell culture platform based on piezoelectric biomaterials for enhanced sEV production. This platform is expected to accelerate the potential use of sEVs for drug delivery and broad biomedical applications.

bioengineering↗

bioRxiv2024

Metatranscriptomic analysis reveals synergistic activities of comammox and anammox bacteria in full-scale attached growth nitrogen removal system.

0-Leveraging comammox Nitrospira and anammox bacteria for shortcut nitrogen removal can drastically lower the carbon footprint of wastewater treatment facilities by decreasing aeration energy, carbon, alkalinity, and tank volume requirements while also potentially reducing nitrous oxide emissions. However, their co-occurrence as dominant nitrifying bacteria is rarely reported in full-scale wastewater treatment. As a result, there is poor understanding of how operational parameters, in particular dissolved oxygen, impact their activity and synergistic behavior. Here, we report the impact of dissolved oxygen concentration (DO = 2, 4, 6 mg/L) on the microbial communitys transcriptomic expression in a full-scale integrated fixed film activated sludge (IFAS) municipal wastewater treatment facility predominantly performed by comammox Nitrospira and anammox bacterial populations. 16S rRNA transcript compositions revealed anammox bacteria and Nitrospira were significantly more active in IFAS biofilms compared to suspended sludge biomass. In IFAS biofilms, anammox bacteria significantly increased hzo expression at lower dissolved oxygen concentrations and this increase was highly correlated with the amoA expression levels of comammox bacteria. Interestingly, the genes involved in nitrite oxidation by comammox bacteria were significantly more upregulated relative to the genes involved in ammonia oxidation with decreasing dissolved oxygen concentrations. Ultimately, our findings suggest that comammox Nitrospira supply anammox bacteria with nitrite via ammonia oxidation and that this synergistic behavior is dependent on dissolved oxygen concentrations. SynopsisComammox bacteria differentially regulate ammonia and nitrite oxidation in response to dissolved oxygen concentration suggesting dissolved oxygen dependence of their synergistic nitrogen removal with anammox bacteria in IFAS biofilms.

microbiology↗

bioRxiv2023

An AAV capsid reprogrammed to bind human Transferrin Receptor mediates brain-wide gene delivery

Developing vehicles that efficiently deliver genes throughout the human central nervous system (CNS) will broaden the range of treatable genetic diseases. We engineered an AAV capsid, BI-hTFR1, that binds human Transferrin Receptor (TfR1), a protein expressed on the blood-brain barrier (BBB). BI-hTFR1 was actively transported across a human brain endothelial cell layer and, relative to AAV9, provided 40-50 times greater reporter expression in the CNS of human TFRC knock-in mice. The enhanced tropism was CNS-specific and absent in wild type mice. When used to deliver GBA1, mutations of which cause Gaucher disease and are linked to Parkinsons disease, BI-hTFR1 substantially increased brain and cerebrospinal fluid glucocerebrosidase activity compared to AAV9. These findings establish BI-hTFR1 as a promising vector for human CNS gene therapy.

neuroscience↗

bioRxiv2023

Transmission failure from olfactory receptor neurons targeting a single glomerulus disrupts odour constancy

The ability to consistently recognise an object despite sensory input that varies with environmental conditions and/or distance from the object is termed perceptual constancy. This is not an innate ability, rather it develops early in life and is likely dependent upon experience (1, 2). The neural mechanisms underpinning the development of perceptual constancy are poorly understood. We have taken advantage of the olfactory system of mice and show that when mice are naive to an odour a perceptual shift occurs with increasing concentration. The perceptual shift coincides with a rapid reduction in activity of a single olfactory receptor channel that is most sensitive to the odour. This drop in activity is not a property of circuit interactions within the olfactory bulb, rather it is due to a sensitivity miss-match of olfactory receptor neurons within the nose. We show that after forming an association of this odour with food, the sensitivity of the receptor channel is matched to the odour object, preventing transmission failure and promoting perceptual stability. These data show that plasticity of the primary sensory organ enables learning of perceptual constancy.

neuroscience↗

bioRxiv2023

Mitochondrial protein FKBP8 captures PDZD8 to form mitochondria-ER contacts

Mitochondria-ER membrane contact sites (MERCS) represent a fundamental ultrastructural feature underlying unique biochemistry and physiology in eukaryotic cells. The ER protein PDZD8 is required for the formation of MERCS in many cell types, however, its tethering partner on the outer mitochondrial membrane (OMM) is currently unknown. Here we identified the OMM protein FKBP8 as the tethering partner of PDZD8 using a combination of unbiased proximity proteomics, CRISPR-Cas9 endogenous protein tagging, Cryo-Electron Microscopy (Cryo-EM) tomography, and correlative light-EM (CLEM). Single molecule tracking revealed highly dynamic diffusion properties of PDZD8 along the ER membrane with significant pauses and capture at MERCS. Overexpression of FKBP8 was sufficient to narrow the ER-OMM distance, whereas independent versus combined deletions of these two proteins demonstrated their interdependence for MERCS formation. Furthermore, PDZD8 enhances mitochondrial complexity in a FKBP8-dependent manner. Our results identify a novel ER-mitochondria tethering complex that regulates mitochondrial morphology in mammalian cells.

cell biology↗

bioRxiv2023

Deep reconstructing generative networks for visualizing dynamic biomolecules inside cells

Advances in cryo-electron tomography (cryo-ET) have produced new opportunities to visualize the structures of dynamic macromolecular machinery in native cellular environments. Here, we describe a machine learning approach that can reconstruct the structural landscape and dynamics of biomolecular complexes present in cryo-ET subtomograms. This method, cryoDRGN-ET, learns a deep generative model of 3D density maps directly from subtomogram tilt series images and can capture states diverse in both composition and conformation. We use this approach to reconstruct the in situ translation dynamics of prokaryotic ribosomes, and we reveal the distribution of functional states during translation elongation populated by S. cerevisiae ribosomes inside cells.

biophysics↗