Biology subjects

Park, J.

Publications and source records attributed to Park, J..

At least 181 records · Page 10Linked to original sources

bioRxiv2025

Multiple stressors in the Anthropocene: Urban evolutionary history modifies sensitivity to the toxic effects of crude oil exposure in killifish

Persistence of wild species in human-altered environments is difficult, in part because challenges to fitness are complex when multiple environmental changes occur simultaneously, which is common in the Anthropocene. This complexity is difficult to conceptualize because the nature of environmental change is often highly context specific. A mechanism-guided approach may help to shape intuition and predictions about complexity; fitness challenges posed by co-occurring stressors with similar mechanisms of action may be less severe than for those with different mechanisms of action. We approach these considerations within the context of ecotoxicology because this field is built upon a rich mechanistic foundation. We hypothesized that evolved resistance to one class of common toxicants would afford resilience to the fitness impacts of another class of common toxicants that shares mechanisms of toxicity. Fundulus killifish populations in urban estuaries have repeatedly evolved resistance to persistent organic pollutants including PCBs. Since PCBs and some of the toxicants that constitute crude oil (e.g., high molecular weight PAHs) exert toxicity through perturbation of AHR signaling, we predicted that PCB resistant populations would also be resilient to crude oil toxicity. Common garden comparative oil exposure experiments, including killifish populations with different exposure histories, showed that most killifish populations were sensitive to fitness impacts (reproduction and development) caused by oil exposure, but that fish from the PCB-resistant population were insensitive. Population differences in toxic outcomes were not compatible with random-neutral expectations. Transcriptomics revealed that the molecular mechanisms that contributed to population variation in PAH resilience were shared with those that contribute to evolved variation in PCB resilience. We conclude that the fitness challenge posed by environmental pollutants is effectively reduced when those chemicals share mechanisms that affect fitness. Mechanistic considerations may help to scale predictions regarding the fitness challenges posed by stressors that may co-occur in human-altered environments.

evolutionary biology↗

bioRxiv2025

An experimental test of the influence of microbial manipulation on sugar kelp (Saccharina latissima) supports the the core influences host function hypothesis

Kelp are valued for a wide range of commercial products and for their role in kelp forest ecosystems, making kelp cultivation a rapidly expanding economic sector. Microbes associated with kelp and other macroalgae play a critical role in processes such as nutrient exchange, chemical signaling, and defense against pathogens. Thus, manipulating the microbiome to enhance macroalgal growth and resilience is a promising yet underexplored approach for sustainable kelp cultivation. The core microbiome hypothesis suggests that the bacteria that are consistently found on a host (the core microbes) are likely to have a disproportionate impact on host biology, making them an attractive target for microbiome manipulation. In this study, we surveyed wild Saccharina latissima and their surrounding environment to identify core bacterial taxa, compared them to cultivated kelp, and experimentally tested how cultured bacterial isolates affect kelp development. We found that core bacteria are nearly absent in cultivated juvenile sporophytes in nurseries but eventually colonized them after outplanting to ocean farm sites. Bacterial inoculants had both positive and negative effects on kelp development. Notably, the strength of association of a bacterial genus with kelp in the wild positively correlated with its impact on gametophyte settlement and sporophyte development in kelp co-culture experiments, aligning with predictions from the core microbiome influences host function hypothesis. These findings affirm the feasibility of using microbial manipulations to improve current kelp aquaculture practices and provide a framework for developing these techniques. IMPORTANCEMicroorganisms consistently associated with hosts are widely thought to be more likely to impact host biology and health. However, this intuitive concept has not been experimentally evaluated. This study formalizes this concept as the Core microbiome Influences Host Function hypothesis and experimentally tests this hypothesis in sugar kelp (Saccharina). The distribution of bacteria on wild kelp and core microbes were first identified by compiling a broad dataset of the kelp microbiome sampled across space and time. Bacterial cultures were isolated from the surface of sugar kelp and individually grown in laboratory co-culture with sugar kelp spores to assess the ability of bacterial isolates to influence kelp growth and development. In support of the core influences host function hypothesis, isolates belonging to bacterial genera that are more strongly associated with wild sugar kelp are more likely to influence development in laboratory experiments.

ecology↗

bioRxiv2025

Compositional architecture: Orthogonal neural codes for task context and spatial memory in prefrontal cortex

The prefrontal cortex (PFC) is crucial for maintaining working memory across diverse cognitive tasks, yet how it adapts to varying task demands remains unclear. Compositional theories propose that cognitive processes in neural network rely on shared components that can be reused to support different behaviors. However, previous studies have suggested that working memory components are task specific, challenging this framework. Here, we revisit this question using a population-based approach. We recorded neural activity in macaque monkeys performing two spatial working memory tasks with opposing goals: one requiring movement toward previously presented spatial locations (look task) and the other requiring avoidance of those locations (no-look task). Despite differences in task demands, we found that spatial memory representations were largely conserved at the population level, with a common low-dimensional neural subspace encoding memory across both tasks. In parallel, task identity was encoded in an orthogonal subspace, providing a stable and independent representation of contextual information. These results provide neural evidence for a compositional model of working memory, where representational geometry enables the efficient and flexible reuse of mnemonic codes across behavioral contexts while maintaining an independent representation of context.

neuroscience↗

bioRxiv2025

Astrocytic MAOB-GABA axis as a molecular brake on repair following spinal cord injury

Neuroregeneration and remyelination rarely occur in the adult mammalian brain and spinal cord following central nervous system (CNS) injury. The glial scar has been proposed as a major contributor to this failure in the regenerative process. However, its underlying molecular and cellular mechanisms remain unclear. Here, we report that monoamine oxidase B (MAOB)-dependent excessive GABA release from reactive astrocytes suppresses CNS repair system by reducing BDNF and TrkB expression in severe spinal cord injury (SCI) animal models. Genetic deletion of MAOB in a mouse SCI model promotes both functional and tissue recovery. Notably, the selective MAOB inhibitor, KDS2010, facilitates recovery and regeneration by disinhibiting the BDNF-TrkB axis in a rat SCI model. Its dose-dependent effects were further validated in a monkey SCI model. Moreover, KDS2010 demonstrates a tolerable safety profile and dose-proportional pharmacokinetics in healthy humans during a phase 1 clinical trial. Our findings identify the astrocytic MAOB-GABA axis as a crucial molecular and cellular brake on CNS repair system following SCI and highlight translational potential of KDS2010 as a promising therapeutic candidate for SCI treatment.

neuroscience↗

bioRxiv2025

Lack of motor defects and ALS-like neuropathology in heterozygous Sptlc1 Exon 2 deletion mice

Mutations in the human SPTLC1 gene have recently been linked to early onset amyotrophic lateral sclerosis (ALS), characterized by global atrophy, motor impairments, and symptoms such as tongue fasciculations. All known ALS-linked SPTLC1 mutations cluster within exon 2 and a specific variant, c.58G>T, results in exon 2 skipping. However, it is unclear how the exon 2 deletion affects SPTLC1 function in vivo and contributes to ALS pathogenesis. Leveraging the high genomic sequence similarity between mouse and human SPTLC1, we created a novel mouse model with a CRISPR/Cas9-mediated deletion of exon 2 in the endogenous murine Sptlc1 locus. While heterozygous mice did not develop motor defects or ALS-like neuropathology, homozygous mutants died prematurely. These findings indicate that Sptlc1 {Delta}Exon2 heterozygous mice do not replicate the disease phenotype but provide valuable insights into SPTLC1 biology and serve as a useful resource for future mechanistic studies.

neuroscience↗

bioRxiv2025

Adult killifish exposure to crude oil perturbs embryonic gene expression and larval morphology in first- and second-generation offspring

Exposures to environmental toxicants can have both immediate and long-term impacts, including those that persist into the next generation. Using Gulf killifish (Fundulus grandis), we tested whether adult progenitor exposure to crude oil caused perturbations to larval morphology and embryonic genome-wide gene expression in their first- and second-generation descendants raised in clean water. We also tracked responses of additional direct oil exposures in the F1 and F2 embryos. Exposure to oil in progenitor fish caused altered larval morphology in F1 and F2 descendants. Some perturbations were enhanced by additional oil exposure in lineages with progenitors that had been exposed to oil. Progenitor exposures altered embryonic gene expression in F1 and F2 descendants, implicating impacts on neurological and cardiovascular systems. Molecular responses to progenitor exposure were distinct between F1 and F2 offspring, suggesting complex interactions between mechanisms that contribute to the transgenerational transfer of information. In contrast, molecular responses to additional direct oil exposures during early-life development were highly conserved between generations and between progenitor exposure treatments. We conclude that exposure to crude oil causes developmental perturbations that propagate at least two generations, and we present additional hypotheses about underlying molecular mechanisms and emergent health consequences. SYNOPSISThis study shows that exposure of adult fish to crude oil perturbs development and gene expression in offspring and grand-offspring, thereby extending the timeframe necessary to consider ecotoxicological risk.

pharmacology and toxicology↗

bioRxiv2025

CAR-T cells locally delivered in porcine decellularized matrix hydrogels enhance survival in post-resection glioblastoma

Patients diagnosed with glioblastoma (GBM) receive a devastating prognosis of less than 15 months, and recurrence of GBM is most often local, suggesting that regional therapies would serve both immediate and long-term needs of patients. Here, we investigate a biomaterials-based approach for local delivery of chimeric antigen receptor (CAR) T cells using a murine model of partial GBM resection that mimics patient recurrence. We demonstrate that hydrogel delivery of CAR T cells directly into the intracranial resection cavity can stably implant cellular immunotherapies against CNS solid tumors, and significantly prolongs survival in recurrent GBM-bearing mice compared to those receiving resection alone. One Sentence SummaryDuring resection surgeries for brain tumors, delivering cell therapy at time of surgery could improve outcomes for patients.

cancer biology↗

bioRxiv2025

Interplay between cytokine and FGF2 signaling in induction of entosis and vasculogenic mimicry response in glioblastoma

Tumor vascularization is critical to survival of cancer cells, but is frequently perturbed leading to disorganized angiogenesis and emergence of alternative means of delivery of oxygen and nutrients, such as vasculogenic mimicry (VM). Understanding of VM and its relationship to endothelial vascularization has been hampered by the lack of comprehensive combination of in vivo clinical data and relevant in vitro models. We address this challenge by analyzing glioblastoma (GBM) tumors and clinically isolated cancer cells. This analysis strongly suggests a key role of macrophage-induced controlled cell death in emergence of VM. The results further point to entosis of cancer cells as a critical intermediate state in this process, enabled by mechano-chemical cell heterogeneity. We find evidence that macrophages can regulate endothelial angiogenesis and VM as two alternative vascularization mechanisms. These results reveal mechanistic underpinnings of VM and pave the way to predictive analysis of tumor progression.

cancer biology↗

bioRxiv2025

Epigenetic dysregulation of metabolic programs mediates liposarcoma cell plasticity

Sarcomas are rare connective tissue cancers thought to arise from aberrant mesenchymal stem cell (MSC) differentiation. Liposarcoma (LPS) holds valuable insights into dysfunctional differentiation given its well- and dedifferentiated histologic subtypes (WDLPS, DDLPS). Despite well-established differences in histology and clinical behavior, the molecular pathways underlying each subtype are poorly understood. Here, we performed single-nucleus multiome sequencing and spatial profiling on carefully curated human LPS samples and found defects in adipocyte-specific differentiation within LPS. Loss of insulin-like growth factor 1 (IGF1) and gain of cellular programs related to early mesenchymal development and glucagon-like peptide-1 (GLP-1)-induced insulin secretion are primary features of DDLPS. IGF1 loss was associated with worse overall survival in LPS patients. Through in vitro stimulation of the IGF1 pathway, we identified that DDLPS cells are deficient in the adipose-specific PPARG isoform 2 (PPARG2). Defects in IGF1/PPARG2 signaling in DDLPS led to a block in differentiation that could not be fully overcome with the addition of exogenous IGF1 or the pro-adipogenic agonists to PPARG and GLP-1. However, we noted upregulation of the IGF1 receptor (IGF1R) in the setting of IGF1 deficiency, which promoted sensitivity to an IGF1R-targeted antibody-drug conjugate that may serve as a novel therapeutic strategy in LPS. In summary, lineage-specific defects in adipogenesis drive dedifferentiation in LPS and may translate into selective therapeutic targeting in this disease.

cancer biology↗

bioRxiv2025

Mouse Single-Cell Long-Read Splicing Atlas by Ouro-Seq

Alternative splicing creates cellular and phenotypic diversity; thus, characterizing splicing patterns across diverse cell types is essential for a comprehensive understanding of these cell types. However, existing full-length single-cell RNA-sequencing methods suffer from multiple technical limitations, such as the pervasive presence of reverse transcription artifacts across genes. Here, we introduce Ouro-Seq, a novel single-cell long-read sequencing framework with a versatile artifact removal mechanism for characterizing full-length mRNA species expressed by individual cells. We also developed a computational pipeline that identifies genuine full-length cDNAs and normalizes full-length mRNA size distributions for integration. Using Ouro-Seq, we constructed the Mouse Single-Cell Long-Read Splicing Atlas by collecting full-length transcriptomes of 103,304 nuclei or cells from 12 major organs and tissues of adult mice. Our atlas comprehensively characterizes alternative splicing, alternative promoter usage, and alternative polyadenylation events across cell types, revealing previously unappreciated functional heterogeneity among individual cells. Different cell types exhibit largely distinct expression patterns of various isoforms, corresponding to their specific morphologies and biological functions. Our splicing atlas and generalized long-read frameworks will empower researchers to fully interpret biological variation across full-length transcriptomes of single cells.

genomics↗

bioRxiv2025

The patient-specific mouse model with Foxg1 frameshift mutation provides insights into the pathophysiology of FOXG1 syndrome

AbstractsSingle allelic mutations in the forebrain-specific transcription factor gene FOXG1 lead to FOXG1 syndrome (FS). To decipher the disease mechanisms of FS, which vary depending on FOXG1 mutation types, patient-specific animal models are critical. Here, we report the first patient-specific FS mouse model, Q84Pfs heterozygous (Q84Pfs-Het) mice, which emulates one of the most predominant FS variants. Remarkably, Q84Pfs-Het mice recapitulate various human FS phenotypes across cellular, brain structural, and behavioral levels, such as microcephaly, corpus callosum agenesis, movement disorders, repetitive behaviors, and anxiety. Q84Pfs-Het cortex showed dysregulations of genes controlling cell proliferation, neuronal projection and migration, synaptic assembly, and synaptic vesicle transport. Interestingly, the FS-causing Q84Pfs allele produced the N-terminal fragment of FOXG1, denoted as Q84Pfs protein, in Q84Pfs-Het mouse brains. Q84Pfs fragment forms intracellular speckles, interacts with FOXG1 full-length protein, and triggers the sequestration of FOXG1 to distinct subcellular domains. Q84Pfs protein also promotes the radial glial cell identity and suppresses neuronal migration in the cortex. Together, our study uncovered the role of the FOXG1 fragment derived from FS-causing FOXG1 variants and identified the genes involved in FS-like cellular and behavioral phenotypes, providing essential insights into the pathophysiology of FS.

neuroscience↗

bioRxiv2025

Deciphering Features of Metalloprotease Cleavage Targets Using Protein Structure Prediction

IntroductionADAM10 (A Disintegrin and Metalloproteinase 10) cleaves specific substrates, influencing diverse physiological and pathological processes. However, its substrate specificity and cleavage sites remain insufficiently characterized. This study aimed to identify and classify substrate features and elucidate cleavage sites using computational approaches. MethodsProtein structure prediction was performed on 13 substrates with experimentally defined cleavage sites to analyze ADAM10-substrate interactions and assess their structural and spatial characteristics. ResultsBased on protein structure prediction of experimentally validated substrates, we identified four recurrent structural features associated with ADAM10-mediated cleavage. First, most substrates were predicted to interact with the proteolytically active form of ADAM10 (92.3%). Second, interaction sites were typically located in the extracellular region rather than intracellular or transmembrane domains (76.9%). Third, cleavage sites predominantly resided in unstructured or extended loop regions, corresponding to linear secondary structures ([~]70%). Lastly, cleavage sites were spatially enriched in octants (1, 4, 5, and 8) relative to the catalytic Zn{superscript 2}{square} ion in the active site (84.0%). These percentages were calculated per determinant. On the basis of these determinants, we developed a classification algorithm and organized 51 substrates accordingly. As a result, 82.4% of the substrates were assigned to either Group 1 (51.0%) or Group 2 (31.4%). DiscussionThis study presents a structure-informed classification approach for predicting ADAM10 cleavage substrates, enabling candidate identification without direct experimental validation. ConclusionsWe present a novel structure-based framework for classifying the substrates of ADAM10 and demonstrate its applicability to other Metalloproteases.

bioinformatics↗

bioRxiv2025

Monoclonal Nanobodies Alter the Activity and Assembly of the Yeast Vacuolar H+-ATPase

The vacuolar ATPase (V-ATPase; V1Vo) is a multi-subunit rotary nanomotor proton pump that acidifies organelles in virtually all eukaryotic cells, and extracellular spaces in some specialized tissues of higher organisms. Evidence suggests that metastatic breast cancers mislocalize V-ATPase to the plasma membrane to promote cell survival and facilitate metastasis, making the V-ATPase a potential drug target. We have generated a library of camelid single-domain antibodies (Nanobodies; Nbs) against lipid-nanodisc reconstituted yeast V-ATPase Vo proton channel subcomplex. Here, we present an in-depth characterization of three anti-Vo Nbs using biochemical and biophysical in vitro experiments. We find that the Nbs bind Vo with high affinity, with one Nb inhibiting holoenzyme activity and another one preventing enzyme assembly. Using cryoEM, we find that two of the Nbs bind the c subunit ring of the Vo on the lumen side of the complex. Additionally, we show that one of the Nbs raised against yeast Vo can pull down human V-ATPase (HsV1Vo). Our research demonstrates Nb versatility to target and modulate the activity of the V-ATPase, and highlights the potential for future therapeutic Nb development.

biochemistry↗

bioRxiv2025

DNA topological regulation by topoisomerase IIbeta-DNA-PK interaction is important for controlled hypoxia-inducible gene expression

Hypoxic stress responses are essential for cellular and organismal survival and drive gene regulation across diverse biological pathways, including cell cycle progression and energy metabolism. Here, we show that topoisomerase II{beta} (TOP2B) regulates DNA topology and transcription of hypoxia-inducible genes (HIGs) in a DNA-dependent protein kinase (DNA-PK)-dependent manner. Integrated cellular, biochemical, and genomic analyses reveal an antagonistic yet correlated relationship between TOP2B and DNA-PK activities. Under normoxic conditions, TOP2B associates with HIGs and represses transcription by suppressing DNA negative supercoiling formation and accessibility. Under hypoxic exposure, TOP2B dissociates from HIGs, while DNA-PK and HIF1 are recruited to activate HIGs. Notably, DNA-PK is required for the repressive function of TOP2B, as DNA-PK knockout abrogates TOP2B release and activity, resulting in elevated expression of a number of HIGs. Mechanistically, DNA-PK phosphorylates TOP2B at T1403, stimulating its catalytic activity to restrain DNA unwinding and accessibility, thereby suppressing HIG transcription. Collectively, these findings identify a novel role for TOP2B and DNA-PK-mediated regulation of TOP2B as key transcriptional regulators of HIG expression. We propose that phosphorylation-dependent modulation of TOP2B activity is coordinated with transcriptional states and determines DNA topology to regulate Pol II transcription.

molecular biology↗

bioRxiv2025

Searching for Sequence Features that Control DNA Cyclizability

The mechanical properties of DNA molecules are crucial in many biological processes, from DNA packaging to transcription regulation. While the mechanics of long DNA typically follow the worm-like chain polymer model, multiple studies have shown that the mechanics of short DNA - at the length scale of DNA-protein interactions - depend strongly on its sequence content. Motivated by recent high-throughput measurements of sequence-dependent DNA cyclizability - the DNAs tendency to mechanically bend and form a loop, we developed a statistical mechanics approach to systematically explore how cyclizability depends on interactions between individual nucleotides in the sequence. By applying this method to datasets of randomly generated and biologically derived sequences, we identified characteristic sequence features that control DNA cyclizability and extracted the most and least cyclizable sequences, the behavior of which we validated through all-atom molecular dynamics simulations. We found that while highly cyclizable sequences share the same periodic features across datasets, distinct sequence patterns can result in low cyclizability. This work contributes to our understanding of the sequence dependence of DNA mechanics and its role in various biological processes, and has implications for the growing field of DNA nanofabrication.

biophysics↗

bioRxiv2024

Probing mechanical selection in diverse eukaryotic genomes through accurate prediction of 3D DNA mechanics

Connections between the mechanical properties of DNA and biological functions have been speculative due to the lack of methods to measure or predict DNA mechanics at scale. Recently, a proxy for DNA mechanics, cyclizability, was measured by loop-seq and enabled genome-scale investigation of DNA mechanics. Here, we use this dataset to build a computational model predicting bias-corrected intrinsic cyclizability, with near-perfect accuracy, solely based on DNA sequence. Further, the model predicts intrinsic bending direction in 3D space. Using this tool, we aimed to probe mechanical selection - that is, the evolutionary selection of DNA sequence based on its mechanical properties - in diverse circumstances. First, we found that the intrinsic bend direction of DNA sequences correlated with the observed bending in known protein-DNA complex structures, suggesting that many proteins co-evolved with their DNA partners to capture DNA in its intrinsically preferred bent conformation. We then applied our model to large-scale yeast population genetics data and showed that centromere DNA element II, whose consensus sequence is unknown, leaving its sequence-specific role unclear, is under mechanical selection to increase the stability of inner-kinetochore structure and to facilitate centromeric histone recruitment. Finally, in silico evolution under strong mechanical selection discovered hallucinated sequences with cyclizability values so extreme that they required experimental validation, yet, found in nature in the densely packed mitochondrial(mt) DNA of Namystynia karyoxenos, an ocean-dwelling protist with extreme mitochondrial gene fragmentation. The need to transmit an extraordinarily large amount of mtDNA, estimated to be > 600 Mb, in combination with the absence of mtDNA compaction proteins may have pushed mechanical selection to the extreme. Similarly extreme DNA mechanics are observed in bird microchromosomes, although the functional consequence is not yet clear. The discovery of eccentric DNA mechanics in unrelated unicellular and multicellular eukaryotes suggests that we can predict extreme natural biology which can arise through strong selection. Our methods offer a way to study the biological functions of DNA mechanics in any genome and to engineer DNA sequences with desired mechanical properties.

biophysics↗

bioRxiv2024

ATF5-Dependent GDF15 Expression Mediates Anesthesia-Induced Neuroprotection Against Stroke

The incidence of perioperative stroke, a rare but severe complication, is increasing in aging populations. Although anesthetics such as sevoflurane may provide protective preconditioning against ischemic injury, clinical outcomes have been inconsistent. In this study, we demonstrated that sevoflurane-induced neuroprotection is associated with the upregulation of genes involved in the mitochondrial unfolded protein response (UPRmt) and mitochondrial bioenergetic metabolism. Our findings emphasize the critical role of ATF5, a key transcription factor, in mediating these protective effects. Specifically, we observed that sevoflurane preconditioning significantly upregulates ATF5 and its downstream target GDF15 - a regulator of mitochondrial function - in the cerebral cortex. Notably, we found that this mechanistic pathway was not activated in the brain of aged mice, suggesting that age-specific strategies may be necessary for reducing the risk of perioperative stroke. Considering the steadily increasing age of patients, therapeutic approaches that enhance mitochondrial function in the aged brain may provide additional protection against perioperative stroke.

neuroscience↗

bioRxiv2024

Top-down attention and Alzheimer's pathology impact cortical selectivity during learning,influencing episodic memory in older adults

Human aging affects the ability to remember new experiences, in part, because of altered neural function during memory formation. One potential contributor to age-related memory decline is diminished neural selectivity -- i.e., a decline in the differential response of cortical regions to preferred vs. non-preferred stimuli during event perception -- yet the factors driving variability in neural selectivity with age remain unclear. We examined the impact of top-down attention and preclinical Alzheimers disease (AD) pathology on neural selectivity during memory encoding in 156 cognitively unimpaired older participants who underwent fMRI while performing a word-face and word-scene associative memory task. Neural selectivity in face- and place-selective cortical regions was greater during events that were later remembered compared to forgotten. Critically, neural selectivity during learning positively scaled with memory-related variability in top-down attention, whereas selectivity negatively related to early AD pathology, evidenced by elevated plasma pTau181. Path analysis revealed that neural selectivity at encoding mediated the effects of age, top-down attention, and pTau181 on associative memory. Collectively, these data reveal multiple pathways that contribute to memory differences among older adults -- AD-independent reductions in top-down attention and AD-related pathology alter the precision of cortical representations of events during experience, with consequences for remembering.

neuroscience↗