Biology subjects

Leung, A.

Publications and source records attributed to Leung, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Acclimation to enhanced photorespiratory conditions increases the effectiveness of C2 photosynthesis in C3-C4 intermediates

- C2 photosynthesis reduces photorespiratory carbon loss by shuttling glycine from mesophyll (M) to bundle sheath (BS) tissues, where glycine decarboxylase (GDC) releases CO2 that accumulates around rubisco. C2 photosynthesis has been considered a constitutive character, but as a metabolic trait, it may acclimate to the rate of photorespiratory glycine production. - We grew eleven species from two eudicot and two grass lineages spanning C3 to C2 phenotypes at 32 {degrees}C days and 200 or 800 {micro}mol mol-1 CO2. Acclimation was assessed using leaf gas exchange, GDC P-protein immunolocalization, M and BS ultrastructure, photosynthetic enzyme activity, and photosynthesis modelling. - Low relative to high growth CO2 enhanced C2-related phenotypes in sub-C2 and C2 species but not C3 or proto-Kranz species. Sub-C2 species positioned chloroplasts closer to mitochondria and had lower modelled BS conductance. C2 species increased rubisco capacity and GDC allocation to the BS. Aspartate aminotransferase activity increased in both sub-C2 and C2 species. - Acclimation to greater photorespiratory conditions strengthens C2 photosynthesis, but only in species whose BS has crossed a threshold of organelle and GDC investment. We hypothesize that acclimation could expose C2-related traits to selection and facilitate the origin of C4 photosynthesis.

plant biology↗

bioRxiv2026

Apollo 3: Multi-Species Genome Curation

We present Apollo 3, a new manual genome annotation tool that integrates with the JBrowse 2 genome browser. Its functionality is inspired by existing manual genome annotation tools such as Apollo, Artemis, and Otter, but uses an updated and more scalable architecture and technology stack. It allows the simultaneous editing of multiple genomes, including the visualization of synteny to inform those annotations. Apollo 3 can be used as a standalone annotation editor, or it can be installed on a server and used collaboratively. We describe the application's design, features, and use cases.

genomics↗

bioRxiv2025

How tp1, an indirect wing steering muscle, stabilizes Drosophila's flight

Flapping flight is inherently unstable, requiring Drosophila to fine-tune their wing motions on a milliseconds timescale. Pioneering studies have shown that the direct steering muscles, which attach to the wing hinge, are important for generating these rapid flight reflexes. Recent connectome data, however, reveal that indirect steering muscles or tension muscles, which alter the mechanics of the thorax, receive some of the same synaptic inputs from the sensory apparatus as the direct steering muscles. This discovery suggests that the indirect steering muscles may also be important for flight control. Here, we show that the indirect tergopleural muscles indeed contribute substantially to stabilization, particularly for large pitch perturbations. We find that for small perturbations (less than 1000 deg/s), flies modulate their wing stroke amplitude to generate lift-based corrective torques, a strategy that has been previously documented. For larger perturbations, however, we observe that Drosophila engage an additional wing degree of freedom--the wing pitch angle--to leverage additional lift and drag forces during the corrective maneuver. Quasi-steady aerodynamic simulations reveal that this strategy minimizes power consumption, anaolgous to how some mammals (including humans) adjust their steady-state gaits in a near energy-optimal manner. Using optogenetics and a control theory framework we demonstrate that the tergopleural muscle is activated by a proportional gain component of a nonlinear PI controller responsible for determining the wing pitch angle during large perturbations. A simplified torsional-spring model for the wing hinge captures the changes in the wing pitch dynamics observed during correction maneuvers by using the tergopleural muscle to adjust the rest angle of the wing. These findings provide a striking example of reflex strategy selection in time-critical behaviors and underscores the vital role of indirect steering muscles in flight stabilization.

neuroscience↗

bioRxiv2025

Systems modeling of mitochondrial dynamics in different exercise regimes

Exercise stimulates skeletal muscle signaling and mitochondrial metabolism. Emerging evidence shows that mitochondrial dynamics (i.e., fission and fusion) could be regulated by exercise. Yet, there are knowledge gaps on the following questions: (i) which upstream signals are necessary and sufficient to bias mitochondria toward fission versus fusion? (ii) How does cellular energy status and ROS partition control between DRP1 and MFN/OPA1? And (iii) which combinations of intensity and duration produce similar cytosolic signals but distinct mitochondrial remodeling? To address these gaps, we developed an integrative computational framework that connects exercise regimens to mitochondria fission-fusion machinery by linking blood-myofiber energetics in cytosol and mitochondria to skeletal muscle signaling network. The influence of three exercise regimen (i.e., sprint, resistance, and endurance) on mitochondrial fission and fusion was simulated. Classified qualitative validation of signaling network model against studies not used in developing the model achieved 80% accuracy. The model predicts regimen-specific dynamics starting with acute DRP1-driven fission during exercise followed by MFN1/2-OPA1-mediated re-fusion as energy stress declines, consistent with a cyclical triage-then-rebuild paradigm. Changes are most pronounced and sustained with endurance, sharp but brief with sprint, and minimal with resistance. Global sensitivity analysis identified AMPK/PGC-1[->]MFN1/2 as dominant fusion drivers, ROS and AMPK[->]MFF/DRP1 as primary fission switches, and Ca{superscript 2}-calmodulin, ERK, and LKB1/AMPK as shared regulators of fission and fusion. Our model also predicts that an endurance base, augmented with 1-2 weekly high intensity interval traning (HIIT)/ sprint interval training (SIT) sessions could maximize AMPK-ROS pulses and mitochondrial fission-fusion. This framework unifies muscles signaling logic with the energetic state to explain how intensity-volume combinations, bout spacing, and kinase modulation tune mitochondrial remodeling, yielding testable predictions for optimizing training and adjuvant therapies for enhanced human performance.

systems biology↗

bioRxiv2025

Convergence, stability, and thermal adaptation in the rubisco enzyme in plants

Enzymes are thought to be tuned to perform similarly in different thermal regimes. Whether the photosynthetic enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) follows similar rules, especially when considering evolutionary history, is uncertain. The molecular, structural, and ecological factors of the rubisco large subunit (RbcL) were examined in four plant clades: wood ferns, pines, sea lavenders, and viburnums. Using rbcL gene sequences, codon evolutionary models were used to test for positive and divergent selection and convergent evolution. Protein structure modeling was performed to predict side chain changes and protein stability. Phylogenetic comparative methods were used to examine the relationship between protein stability to growing season temperature. All four clades showed significant evidence of positive selection, with multiple convergent substitutions predicted to alter side chain polarity and interactions with the solvent. In viburnums, biome transition rates were dependent on amino acid substitution, with positive selection was concentrated in cold temperate and cloud forest clades. Rubiscos with higher stability occurred in species from warmer environments. However, this correlation was weaker after correcting for phylogeny. These analyses support a hypothesis that RbcL evolution is influenced by both environmental tuning and evolutionary history.

plant biology↗

bioRxiv2025

Plasmodium falciparum DNA repair dynamics reveal unique roles for TLS polymerases and PfRad51 in genome diversification

The haploid malaria parasite, Plasmodium falciparum, evolved a unique cohort of DNA repair pathways enabling the parasite to survive in a vertebrate host red blood cell and the mosquito vector. P. falciparum chromosomes are partitioned into a highly conserved core genome and remarkably diverse, largely subtelomeric regions that contain genes encoding important parasite virulence factors. The molecular mechanisms that maintain this chromosomal structure have not been identified. Here, we describe specific DNA repair pathways that differentiate between hypervariable subtelomeric and conserved core regions of the genome. Based on our previous work, we hypothesized that there are potentially important interactions between translesion (TLS) and homologous recombination (HR) pathways for the diversification of multicopy gene families in P. falciparum. Thus, we created knockout parasite lines of the DNA repair enzymes: PfRad51 and the TLS polymerases PfPol{zeta} and PfRev1. We identified that irradiation hypersensitivity varied across the cell cycle for TLS{Delta} parasites and was uniform across the erythrocytic cycle for PfRad51{Delta} parasites, highlighting the variable roles of these pathways. However, important interactions between these pathways were found when we studied directed double strand break (DSB) repair, which revealed a difference in the DNA damage response according to chromosomal location. PfRad51 was essential for HR-mediated repair in the core genome. In contrast, we identified a Rad51 independent homology-directed repair in all three of our knockout lines when a DSB was made in the subtelomeric region of the chromosome. We propose that this differential DNA damage response maintains the distinction in diversification across the chromosome.

microbiology↗

bioRxiv2025

Functional and structural characterization of a combination of pan-sarbecovirus antibodies with potent antiviral activity

Sarbecoviruses, a subgenus of coronaviruses, include strains with zoonotic spillover risk as exemplified by recent outbreaks (SARS-CoV-1, SARS-CoV-2). Monoclonal antibodies targeting conserved spike protein regions (RBD class 4, S2 fusion machinery) exhibit broad sarbecovirus neutralization, but their utility has been impacted by immune selection leading to escape and suboptimal neutralization. Using structure-conditioned machine-learning protein design we optimized two broadly neutralizing sarbecovirus antibodies to rescue the activity of a class 4 anti-RBD antibody against Omicron variants and improve the neutralization profile of an anti-S2 stem antibody, resulting in the identification of the lead candidates PRO-37587 and GB-0669. Both antibodies displayed remarkable resilience to SARS-CoV-2 evolution. Structural analyses elucidated the mechanistic basis of their broad neutralization profiles. In combination, these antibodies exhibited improved SARS-CoV-2 neutralization in vitro and in vivo and a higher barrier to resistance. These findings support further evaluation of such antibody combination as countermeasure against current and emerging sarbecoviruses.

microbiology↗

bioRxiv2024

Directionality of Transcriptional Regulatory Elements

Divergent transcription is a critical marker of active transcriptional regulatory elements (TREs), including enhancers and promoters, in mammals. However, distal elements with unidirectional transcriptional patterns are often overlooked, leaving their identity and function poorly understood. Here, we performed a systematic comparison between divergent and unidirectional elements, revealing their distinct architectural and functional features. Our analysis also shows that unidirectional elements have younger sequence ages and are under weaker evolutionary constraints than divergent elements, indicating that they may represent a unique category of genomic regulatory function with more recent origins. Notably, we observed that some transcription factors, including CTCF, AP1, SP, and NFY, exhibit dual roles in modulating the directionality of TREs, either activating or repressing nascent transcription in a position-dependent manner. Overall, the elucidation of directionality enhances our understanding of the diverse architectural models, functional features, evolutionary dynamics, and regulatory logic of TREs.

molecular biology↗

bioRxiv2024

Fc-engineered large molecules targeting blood-brain barrier transferrin receptor and CD98hc have distinct central nervous system and peripheral biodistribution compared to standard antibodies

The blood-brain barrier (BBB) poses a significant challenge drug delivery to the brain. BBB-crossing molecules are emerging as a new class of therapeutics with significant potential for central nervous system (CNS) indications. In particular, transferrin receptor (TfR)- and CD98 heavy chain (CD98hc)-targeting molecules have been demonstrated to cross the BBB for enhanced brain delivery. Previously, we reported TfR and CD98hc antibody transport vehicles (ATVTfR and ATVCD98hc) that utilize these BBB receptors to improve CNS drug delivery1,2. Here, we provide a comprehensive and unbiased biodistribution characterization of ATVTfR and ATVCD98hc compared to a standard IgG at a multiscale level, ranging from whole-body to brain region- and cell type-targeting specificity. Mouse whole-body tissue clearing revealed distinct organ localization for each molecule. In the CNS, ATVTfR and ATVCD98hc not only achieves enhanced brain delivery but importantly, much broader parenchymal distribution in contrast to the severely limited distribution observed with a standard antibody that was not able to be improved even at very high dose levels. Using cell sorting and single-cell RNA sequencing of mouse brain, we revealed that standard IgG predominantly localizes to perivascular and leptomeningeal cells and reaches the CNS by entering the CSF, rather than crossing the BBB. In contrast, ATVTfR and ATVCD98hc enables broad parenchymal cell-specific distribution via transcytosis through brain endothelial cells (BECs) along the neurovasculature. Finally, we extended the translational relevance of our findings by revealing enhanced and broad brain and spinal cord biodistribution of ATVTfR compared to standard IgG in cynomolgus monkey. Taken together, this multiscale analysis reveals in-depth biodistribution differences between ATVTfR, ATVCD98hc, and standard IgG. These results may better inform platform selection for specific therapeutic targets of interest, optimally matching platforms to desired CNS target engagement, peripheral organ exposures, and predict or potentially reduce off-target effects.

neuroscience↗

bioRxiv2024

SEM-2/SoxC regulates multiple aspects of C. elegans postembryonic mesoderm development

Development of multicellular organisms requires well-orchestrated interplay between cell-intrinsic transcription factors and cell-cell signaling. One set of highly conserved transcription factors that plays diverse roles in development is the SoxC group. C. elegans contains a sole SoxC protein, SEM-2. SEM-2 is essential for embryonic development, and for specifying the sex myoblast (SM) fate in the postembryonic mesoderm, the M lineage. We have identified a novel partial loss-of-function sem-2 allele that has a proline to serine change in the C-terminal tail of the highly conserved DNA-binding domain. Detailed analyses of mutant animals harboring this point mutation uncovered new functions of SEM-2 in the M lineage. First, SEM-2 functions antagonistically with LET-381, the sole C. elegans FoxF/C forkhead transcription factor, to regulate dorsoventral patterning of the M lineage. Second, in addition to specifying the SM fate, SEM-2 is essential for the proliferation and diversification of the SM lineage. Finally, SEM-2 appears to directly regulate the expression of hlh-8, which encodes a basic helix-loop-helix Twist transcription factor and plays critical roles in proper patterning of the M lineage. Our data, along with previous studies, suggest an evolutionarily conserved relationship between SoxC and Twist proteins. Furthermore, our work identified new interactions in the gene regulatory network (GRN) underlying C. elegans postembryonic development and adds to the general understanding of the structure-function relationship of SoxC proteins. AUTHOR SUMMARYSoxC transcription factors play important roles in metazoan development. Abnormal expression or function of SoxC factors has been linked to a variety of developmental disorders and cancers. It is therefore critical to understand the functions of SoxC proteins in vivo. C. elegans has a single SoxC transcription factor, SEM-2, that is known to regulate a fate decision between a proliferative progenitor cell vs. a terminally differentiated cell during postembryonic mesoderm development. In this study, we report new functions of SEM-2 in postembryonic mesoderm development via our studies of a partial loss-of-function allele of sem-2. Our work uncovers new regulatory relationships between SEM-2/SoxC and the FoxF/C transcription factor LET-381, and between SEM-2/SoxC and the C. elegans Twist ortholog HLH-8. Our findings suggest that the SoxC-Twist axis, including the downstream targets of Twist, represents an evolutionarily conserved regulatory cassette important in metazoan development.

developmental biology↗

bioRxiv2024

Proteogenomic Reprogramming to a Functional Human Totipotent Stem Cell State via a PARP-DUX4 Regulatory Axis

PARP1 (ARTD1) and Tankyrases (TNKS1/TNKS2; PARP5a/5b) are poly-ADP-ribose polymerases (PARPs) with catalytic and non-catalytic functions that regulate both the genome and proteome during zygotic genome activation (ZGA), totipotent, and pluripotent embryonic stages. Here, we show that primed, conventional human pluripotent stem cells (hPSC) cultured continuously under non-specific TNKS1/TNKS2/PARP1-inhibited chemical naive reversion conditions underwent epigenetic reprogramming to clonal blastomere-like stem cells. TIRN stem cells (TIRN-SC) concurrently expressed hundreds of gene targets of the ZGA-priming pioneer factor DUX4, as well as a panoply of four-cell (4C)-specific (e.g., TPRXL, HOX clusters), eight-cell (8C)-specific (e.g., DUXA, GSC, GATA6), primitive endoderm-specific (e.g., GATA4, SOX17), trophectoderm-specific (e.g., CDX2, TFAP2C), and naive epiblast-specific (e.g., DNMT3L, NANOG, POU5F1(OCT4)) factors; all in a hybrid, combinatorial single-cell manner. Mapping of proteomic and single-cell expressions of TIRN-SC against human preimplantation embryo references identified them as relatively homogenous 4C-8C stage populations. Injection of TIRN cells into murine 8C-16C-staged embryos resulted in efficient totipotent-like single cell contributions of human cells to both extra-embryonic (trophectoderm, placenta) and embryonic (neural, fetal liver, hematopoietic) lineages in human-murine blastocyst and fetal chimeras. Pairing of proteome with ubiquitinome analyses of TIRN-SC revealed a global shutdown of ADP-ribosylation, and a perturbed TNKS/PARP1 equilibrium which not only impacted the protein levels of hundreds of TNKS/PARP1 substrates via a rewiring of the ubiquitin-proteosome system (UPS), but also de-repressed expression of hundreds of developmental genes associated with PARP1 suppression. ChIP-Seq analysis of core NANOG-SOX2-OCT4 (NSO) pluripotency factors in TIRN-SC identified reprogrammed DUX4-accessible distal and cis-regulatory enhancer regions that were co-bound by PARP1 (NSOP). These NSOP enhancer regions possessed co-binding motifs for hundreds of the same ZGA-associated, embryonic, and extraembryonic lineage-specifying pioneer factors (e.g., HOX, FOX, GATA, SOX, TBX, CDX families) that were concurrently co-expressed in TIRN-SC; suggesting that PARP1 and DUX4 cooperate with NSO pluripotency core factors to regulate the epigenetic plasticity of a human totipotency program. These findings provide the first demonstration that global, proteome-wide perturbations of post-translational modifications (i.e., ADP-ribosylation, ubiquitination) can regulate epigenetic reprogramming during human embryogenesis. Totipotent TIRN-SC will provide a valuable cell culture model for studying the proteogenomic regulation of lineage specification from human blastomere stages and may facilitate the efficient generation of human organs in interspecies chimeras.

developmental biology↗

bioRxiv2024

PARP1 condensates differentially partition DNA repair proteins and enhance DNA ligation

Poly(ADP-ribose) polymerase 1 (PARP1) is one of the first responders to DNA damage and plays crucial roles in recruiting DNA repair proteins through its activity - poly(ADP-ribosyl)ation (PARylation). The enrichment of DNA repair proteins at sites of DNA damage has been described as the formation of a biomolecular condensate. However, it is not understood how PARP1 and PARylation contribute to the formation and organization of DNA repair condensates. Using recombinant human PARP1 in vitro, we find that PARP1 readily forms viscous biomolecular condensates in a DNA-dependent manner and that this depends on its three zinc finger (ZnF) domains. PARylation enhances PARP1 condensation in a PAR chain-length dependent manner and increases the internal dynamics of PARP1 condensates. DNA and single-strand break repair proteins XRCC1, LigIII, Pol{beta}, and FUS partition in PARP1 condensates, although in different patterns. While Pol{beta} and FUS are both homogeneously mixed within PARP1 condensates, FUS enrichment is greatly enhanced upon PARylation whereas Pol{beta} partitioning is not. XRCC1 and LigIII display an inhomogeneous organization within PARP1 condensates; their enrichment in these multiphase condensates is enhanced by PARylation. Functionally, PARP1 condensates concentrate short DNA fragments and facilitate compaction of long DNA and bridge DNA ends. Furthermore, the presence of PARP1 condensates significantly promotes DNA ligation upon PARylation. These findings provide insight into how PARP1 condensation and PARylation regulate the assembly and biochemical activities in DNA repair foci, which may inform on how PARPs function in other PAR-driven condensates.

biochemistry↗

bioRxiv2023

Stress-induced endogenous-dsRNAs drive beta-cells to IFN-I state

Aims/hypothesisEndogenous dsRNAs originating from retrotransposons within the human genome have the potential to trigger autoimmunogenic recognition via RIG-like receptors such as MDA5. This phenomenon, known as "viral mimicry", induces potent interferon-beta expression, resulting in cell death and potential collateral death to surrounding cells. Viral mimicry has been mostly studied in relation to epigenetic therapeutics, although there are indications the phenomenon is relevant in other physiological contexts. Here, we demonstrate that proinflammatory cytokine stress leads to the dysregulation of retrotransposons in human beta-cells, resulting in beta-cell death via viral mimicry. MethodsHuman islets from donors were treated with/without proinflammatory cytokines (IFN-{gamma}, TNF-, IL-1{beta}) and immunostained for dsRNA. Publicly available transcriptome and chromatin accessibility data from proinflammatory cytokine treated EndoC-{beta}H1 cells were analyzed to examine changes in transcriptional regulatory activity at retrotransposon loci. Transcriptome profiling experiments in 1.1B4 and MIN6 cells were performed to examine the generality of the results. Adenosine to inosine (A-to-I) editing was compared between sample groups to gauge the extent of RNA editing on dsRNAs. Additional transcriptome data from normal vs. type 1 diabetic human islets was also assessed for differences in A-to-I editing activity between sample groups. ResultsProinflammatory cytokine stress increases the amount of dsRNA in human islets, co-incident with cells that express insulin. In the EndoC-{beta}H1 human beta-cell line, proinflammatory cytokine stress leads to a substantial increase in transcription at RTE loci, including SINE/Alu elements and LINE elements, along with increased expression of RLRs (including MDA5), inflammatory transcription factors (e.g. IRF3, STAT1), and most critically, IFNB1, a potent instigator of type 1 interferon responses. Similar trends were observed in 1.1B4 and MIN6 cells. Gene ontology analysis revealed an enrichment of genes related to interferon signaling and inflammation. Inflammatory stress furthermore leads to an increase in chromatin accessibility at many RTE loci, with enrichment in a variety of RTE subfamilies (including L1, AluY, AluSp, AluSq2, and AluSc elements). Binding sites for inflammatory transcription factors, such as IRFs, are also enriched at these loci. While inflammatory stress increased the overall A-to-I editing events at Alu elements, the pool of total unedited Alus was increased upon inflammatory stress. Examination of A-to-I editing in RNA-seq data from type 1 diabetic human islets and normal controls revealed that editing in diabetic islets is dramatically lower ([~]1%) than islets from normal controls ([~]15%). Conclusions/interpretationTranscription and chromatin accessibility are both increased at RTEs (notably Alus) upon proinflammatory cytokine stress, accompanied by an increase in RLR expression and a shift to a type I interferon state, as indicated by increased IFNB1 and other interferon-stimulated genes, including MDA5, an RLR gene which is also a type 1 diabetes risk gene. The overall increase in A-to-I editing upon inflammatory stress is associated with increases in ADAR1 expression, yet the increase in overall unedited Alus shows that cytokine stress leads to a higher dsRNA burden in the beta-cell. This increase in dsRNA burden is further compounded by increased MDA5 expression, exacerbating the inflammatory state of the beta-cell. Comparisons of A-to-I editing between normal vs. type 1 diabetic human islets suggest that type 1 diabetics have more unedited dsRNAs, hindering their ability to prevent autoimmunogenic recognition. Research in contextWhat is already known about this subject? O_LICytokine stress during insulitis is a feature of autoimmune diabetes. C_LIO_LIStress-induced dysregulation of retrotransposons can lead to a dsRNA-based type-I interferon response in a variety of cells ( viral mimicry) C_LIO_LIEndogenous dsRNAs are subject to adenine to inosine (A-to-I) editing by ADAR1 to prevent self-recognition. C_LI What is the key question? O_LICan cytokine stress drive beta-cells into an IFN-I state via recognition of endogenous dsRNAs derived from retrotransposons that lose silencing under cytokine stress? C_LI What are the new findings? O_LICytokine stress causes an increase in dsRNAs derived from retrotransposons in beta-cells from human islets. C_LIO_LIThe SINE/Alu subset of these endogenous dsRNAs are less edited in stressed beta-cells, making them more self-recognizable. C_LIO_LIType 1 diabetic human islets exhibit more unedited Alus. C_LI How might this impact on clinical practice in the foreseeable future? O_LIInnate autoimmunity via endogenous dsRNAs can cause damage to beta-cells; therapies to target this pathway may help treat autoimmune diabetes. C_LI

molecular biology↗

bioRxiv2023

Length-dependent Intramolecular Coil-to-Globule Transition in Poly(ADP-ribose) Induced by Cations

Poly(ADP-ribose) (PAR), a non-canonical nucleic acid, is essential for DNA/RNA metabolism and protein condensation, and its dysregulation is linked to cancer and neurodegeneration. However, key structural insights into PARs functions remain largely uncharacterized, hindered by the challenges in synthesizing and characterizing PAR, which are attributed to its length heterogeneity. A central issue is how PAR, comprised solely of ADP-ribose units, attains specificity in its binding and condensing proteins based on chain length. Here, we integrate molecular dynamics simulations with small-angle X-ray scattering to analyze PAR structures. We reveal the diverse structural ensembles of PAR and the factors influencing them, including a notable length-dependent compaction of PAR upon the addition of small amounts of Mg2+ ions. Unlike PAR15, PAR22 forms ADP-ribose bundles via local intramolecular coil-to-globule transitions. Understanding these length-dependent structural changes could be central to deciphering the specific biological functions of PAR.

biophysics↗

bioRxiv2023

PARP10 is Critical for Stress Granule Initiation

Stress granules (SGs) are cytoplasmic biomolecular condensates enriched with RNA, translation factors, and other proteins. They form in response to stress and are implicated in various diseased states including viral infection, tumorigenesis, and neurodegeneration. Understanding the mechanism of SG assembly, particularly its initiation, offers potential therapeutic avenues. Although ADP-ribosylation plays a key role in SG assembly, and one of its key forms--poly(ADP-ribose) or PAR--is critical for recruiting proteins to SGs, the specific enzyme responsible remains unidentified. Here, we systematically knock down the human ADP-ribosyltransferase family and identify PARP10 as pivotal for SG assembly. Live-cell imaging reveals PARP10s crucial role in regulating initial assembly kinetics. Further, we pinpoint the core SG component, G3BP1, as a PARP10 substrate and find that PARP10 regulates SG assembly driven by both G3BP1 and its modeled mechanism. Intriguingly, while PARP10 only adds a single ADP-ribose unit to proteins, G3BP1 is PARylated, suggesting its potential role as a scaffold for protein recruitment. PARP10 knockdown alters the SG core composition, notably decreasing translation factor presence. Based on our findings, we propose a model in which ADP-ribosylation acts as a rate-limiting step, initiating the formation of this RNA-enriched condensate. HIGHLIGHTSO_LIPARP10 plays a crucial role in the initial SG assembly kinetics. C_LIO_LIThe core SG component G3BP1 is a substrate of PARP10. C_LIO_LIPARP10 is required for SG assembly mediated by G3BP1 or its synthetic mimic. C_LIO_LIPARP10 knockdown reduces the levels of translation factors within the SG core. C_LI

cell biology↗

bioRxiv2023

Autoencoder-transformed transcriptome improves genotype-phenotype association studies

Transcriptome-wide association study (TWAS) is an emerging model leveraging gene expressions to direct genotype-phenotype association mapping. A key component in TWAS is the prediction of gene expressions; and many statistical approaches have been developed along this line. However, a problem is that many genes have low expression heritability, limiting the performance of any predictive model. In this work, hypothesizing that appropriate denoising may improve the quality of expression data (including heritability), we propose AE-TWAS, which adds a transformation step before conducting standard TWAS. The transformation is composed of two steps by first splitting the whole transcriptome into co-expression networks (modules) and then using autoencoder (AE) to reconstruct the transcriptome data within each module. This transformation removes noise (including nonlinear ones) from the transcriptome data, paving the path for downstream TWAS. We showed two inspiring properties of AE-TWAS: (1) After transformation, the transcriptome data enjoy higher expression heritability at the low-heritability spectrum and possess higher connectivity within the modules. (2) The transferred transcriptome indeed enables better performance of TWAS; and moreover, the newly formed highly connected genes (i.e., hub genes) are more functionally relevant to diseases, evidenced by their functional annotations and overlap with TWAS hits.

bioinformatics↗

bioRxiv2022

Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling

Neuronal energy consumption is vital for information processing and memory formation in synapses. The brain consists of just 2% of the human bodys mass, but consumes almost 20% of the bodys energy budget. Most of this energy is attributed to active transport in ion signaling, with calcium being the canonical second messenger of synaptic transmission. Here, we develop a computational model of synaptic signaling resulting in the activation of two protein kinases critical in metabolic regulation and cell fate, AMP-Activated protein kinase (AMPK) and mammalian target of rapamycin (mTOR) and investigate the effect of glutamate stimulus frequency on their dynamics. Our model predicts that frequencies of glutamate stimulus over 10 Hz perturb AMPK and mTOR oscillations at higher magnitudes by up to 70% and area under curve (AUC) by 10%. This dynamic difference in AMPK and mTOR activation trajectories potentially differentiates high frequency stimulus bursts from basal neuronal signaling leading to a downstream change in synaptic plasticity. Further, we also investigate the crosstalk between insulin receptor and calcium signaling on AMPK and mTOR activation and predict that the pathways demonstrate multistability dependent on strength of insulin signaling and metabolic consumption rate. Our predictions have implications for improving our understanding of neuronal metabolism, synaptic pruning, and synaptic plasticity. Key PointsO_LINeurons consume disproportionate amounts of cellular energy relative to their mass, indicating the importance of energy regulation in information processing in the brain. C_LIO_LIAMP activated protein kinase (AMPK) is thought to be the biochemical link between energy consumption in neuronal information processing and synaptic plasticity. C_LIO_LIComputational model investigating the crosstalk between high-frequency glutamatergic calcium signaling and AMPK activation in neurons predicts multistability in AMPK and mammalian target of rapamycin (mTOR) activation. C_LIO_LIOur models predict a frequency-dependent response in AMPK and mTOR activation that also scales according to insulin signaling and energy consumption. The oscillatory behavior depends on both intracellular and extracellular factors, such as energy consumption and insulin signaling. C_LIO_LIThis work elucidates the role of insulin and insulin resistance in regulating neuronal activity, through computational modeling the metabolic response of energy stress resulting from calcium signaling. C_LI

systems biology↗

bioRxiv2022

JBrowse 2: A modular genome browser with views of synteny and structural variation

We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. JBrowse 2 retains the core features of the open-source JavaScript genome browser JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. The software readily allows users to share sessions, open multiple genomes or views, and navigate quickly between these views. It can be embedded in a web page, used as a standalone desktop application, or run from Jupyter notebooks or R sessions. Using a plugin framework, developers can create new data adapters, track types, and visualizations. These improvements are enabled by a ground-up redesign of the JBrowse architecture using modern web technology. We describe application functionality, use cases, performance benchmarks, and implementation notes for web administrators and developers.

bioinformatics↗