Biology subjects

Kim, H. S.

Publications and source records attributed to Kim, H. S..

At least 19 recordsLinked to original sources

bioRxiv2026

Deep learning-based counting and body-area measurement enable sensitive population-level endpoints in the Collembola reproduction test

Springtails (Collembola) are standard test organisms for soil ecotoxicological assessment; under the ISO 11267 and OECD 232 guidelines, adult abundance and juvenile production are the primary endpoints. However, these rely on labor-intensive manual counting and capture only abundance, overlooking sublethal effects on growth. We developed an automated system that couples YOLOv8 object detection with Voronoi-Otsu segmentation-based body-area measurement, so that adults and juveniles of Allonychiurus kimi are counted and their growth (body area) measured simultaneously, and applied it to toxicity assessment based on average and cumulative body area and to cohort analysis of juvenile body-area distributions using a Gaussian mixture model (GMM). The model was trained on 142 annotated images and validated on 160 images from toxicity tests with cadmium (Cd), arsenic (As), and copper (Cu), and both detection accuracy and agreement with manual measurements were excellent (coefficient of determination, R2 >= 0.95). Cumulative body area, a composite indicator integrating abundance and individual size and thus reflecting both reproduction and growth, showed the lowest EC50 in all three metal(loid)s (Cd 14.10, As 10.53, Cu 398.80 mg kg-1). Cohort analysis showed that the two cohorts present in the controls merged into one at the highest concentrations (As 20, Cu 800 mg kg-1), indicating that toxic stress drives not only individual-level suppression of reproduction and growth but also population restructuring. Beyond accurately and efficiently replacing manual counting, the system adds more sensitive composite endpoints and population-level analysis, providing a more comprehensive, scalable framework for soil ecotoxicological risk assessment.

ecology↗

bioRxiv2026

Voice and linguistic features support early attentional filtering of irrelevant stimuli

In cocktail party-type environments, listeners must segregate simultaneous acoustic sources and select one for processing. Behavioral studies have established that both low-level voice differences (e.g., pitch) and high-level linguistic differences (e.g., word content) aid these processes. Electroencephalography (EEG) studies have demonstrated that the brain filters voices based on low-level features early in sensory processing, but it is unclear whether linguistic differences also support early filtering. In this EEG study, listeners attended to a lateralized auditory stream of target syllables while ignoring distractor stimuli from the opposite hemifield. In contrast to previous auditory attention studies, target stimuli were always attended and statistically identical across conditions; instead, we manipulated the distractors. Specifically, we manipulated whether targets and distractors were spoken in the same voice or different voices, as well as whether they were composed of the same or different linguistic content. Critically, distractors were temporally offset from targets, enabling an investigation of whether acoustically matched, always attended target stimuli are differentially encoded as a function of surrounding context. Differences in either voice or linguistic features supported target recall: Recall was poor only when both streams were in the same voice and had similar linguistic content. However, voice and linguistic features had independent, additive effects on neural processing. Specifically, target dissimilarity in acoustics and linguistic content both contributed to more robust, larger-magnitude target-evoked EEG responses. Overall, results demonstrate that both linguistic dissimilarity and low-level acoustic dissimilarity improve early attentional filtering of distractors in multi-source acoustic scenes.

neuroscience↗

bioRxiv2026

Effects of vapor inhalation of 6-methyl nicotine in female and male rats

Background: The nicotine analog 6-methyl nicotine (6-MN) has appeared in commercial e-cigarette liquids, and other products, spurring interest in determining the extent to which it conveys similar effects to those of nicotine. Objective: To determine if 6-MN acts like nicotine to decrease body temperature, decrease nociception, suppress wheel activity and reinforce operant behavior when delivered by vapor inhalation using an Electronic Nicotine Delivery System (ENDS; "e-cigarette") approach in a rat model. Methods: Male and female (N=8 per sex) young adult Sprague-Dawley rats were evaluated for rectal temperature and nociceptive responses (warm water tail-withdrawal) to the inhalation of vapor from (-)-6-MN or (-)-nicotine in concentrations ranging from 5-30 mg/mL in the propylene glycol vehicle. Rats were then assessed for the reinforcing effects of nicotine and 6-MN using a vapor self-administration procedure and the rate suppressing effects of nicotine and 6-MN on wheel activity following injection. Results: Inhalation of nicotine or 6-MN for 30 minutes decreased the rectal temperature and increased tail-withdrawal latency of female and male rats in a concentration-dependent manner. The magnitude of the effects of 6-MN and nicotine were similar at similar vapor concentrations. Operant responding for 6-MN vapor was increased by pre-treatment with the antagonist mecamylamine. 6-MN was more potent than nicotine at suppressing wheel activity after injection. Conclusions: 6-MN induces effects very similar to those of nicotine, at a similar potency when inhaled and at a slightly increased potency when injected.

pharmacology and toxicology↗

bioRxiv2026

Time-restricted eating promotes sustained fat loss in Drosophila

While current therapeutics restricting calorie intake, such as GLP-1 agonists, induce fat loss for many people, they are ineffective for others and concerns remain about their long-term effects on health, particularly loss of lean muscle mass. Moreover, many quickly regain fat if they stop treatment. In contrast, time-restricted eating does not restrict calorie intake but instead restricts the time window for eating and prevents obesity in mice and humans. Here we investigated the effects of intermittent Time-Restricted Feeding (iTRF), which extends lifespan and delays markers of aging, on stored fat in Drosophila. Ten days of iTRF caused significant fat loss relative to ad lib diet, an effect that persisted even after return to ad lib diet. Unlike iTRF-induced lifespan extension, iTRF-induced fat loss did not depend on circadian-regulated autophagy. iTRF treated both diet-induced and genetically induced obesity and significantly reduced lipid droplet size in the fat body (adipose tissue). Instead of causing muscle loss, iTRF increased total and muscle-specific protein levels and enhanced flight performance, suggesting a shift in body composition. We found that iTRF evoked fasting-induced hyperactivity, partially mediated by octopamine, the fly ortholog of the human stress hormone norepinephrine. Ablation of octopaminergic neurons (OANs) prevented iTRF-mediated effects: fat loss, increased protein, and enhanced flight performance. Our results suggest that Drosophila iTRF causes rapid, permanent fat loss and increased muscle function through a "fight or flight" response. Understanding the mechanisms driving differences between Drosophila and human responses to TRE could be critical for identifying effective therapeutic targets for obesity.

physiology↗

bioRxiv2026

Investigating Invariances in Auditory Event Categorization with Model Metamers

Real-world acoustic inputs contain rich sensory information that we parse into discrete auditory objects and categories. Although deep neural networks (DNNs) are increasingly used to model auditory perception, the field lacks rigorous behavioral benchmarks, particularly for auditory event categorization. Here, we developed a 25-way categorization paradigm for broad classes of natural sounds to test whether categorical invariances of DNNs align with those of human observers. We first confirmed that humans could reliably categorize the natural sounds, demonstrating that our paradigm is well-suited for testing invariances in auditory categories. To probe model invariances, we evaluated human recognition of model metamers (synthetic stimuli matched to the models internal activations for each natural stimulus) for a wide range of architectures trained on speech or auditory event recognition. Evaluating widely-used public models, we found that human recognition of auditory event model metamers was generally influenced by the training task and data distribution; speech models trained on standard, curated datasets produced less recognizable metamers than auditory event recognition models. We additionally analyzed a controlled set of models to directly investigate the influence of training task and adversarial training, revealing that improved metamer recognition induced by adversarial training is task-dependent. However, even in the best-performing models, we observed a sharp decline in human recognition at the final classification layer compared to the penultimate representation layer. Overall, our results suggest that while invariances in modern architectures better align with human observers for auditory event categorization, there is still a large discrepancy between the categorical invariances of auditory neural networks and the invariances of human observers. Code and models are available at https://github.com/Feather-Lab/env-sound-metamers

neuroscience↗

bioRxiv2026

Patient-Derived Liver Cancer Organoids Reflect Tumor Biology and Their Growth Phenotype Correlates with Clinical Outcomes

Liver cancer remains a major global health burden with high mortality and limited treatment response prediction tools. Patient-derived cancer organoids have emerged as promising preclinical models that recapitulate tumor heterogeneity; however, the biological significance of morphological diversity within established organoids remains poorly characterized in hepatocellular carcinoma (HCC). In this exploratory study, we investigated whether distinct organoid growth phenotypes reflect underlying tumor biology and correlate with clinical outcomes. We established liver cancer organoids from resected tumor tissues of 27 patients and analyzed their clinical, histological, and genomic characteristics. Organoids were classified morphologically into cystic and solid types. Whole exome sequencing (WES) was conducted on six matched tumor-organoid pairs to assess genomic fidelity. Associations between organoid establishment, growth characteristics, and clinical parameters were statistically evaluated. Progression-free survival (PFS) was analyzed using the Kaplan-Meier method and univariate Cox proportional hazards regression. Organoids were successfully established in 13 of 27 cases (48.1%). Solid-type organoids were significantly associated with shorter PFS compared to cystic types (HR = 13.91; p = 0.0039, log-rank test). Organoid establishment was more frequent in older patients (>70 years), those with HBV infection, and tumors with positive {beta}-catenin expression. WES analysis demonstrated high concordance in somatic mutation profiles and variant allele frequency distributions between tissues and corresponding organoids. In univariate Cox regression, organoid growth pattern (solid vs. cystic) showed a significant association with PFS within this exploratory cohort (p = 0.0207). Patient-derived liver cancer organoids preserved the genomic and histopathological features of the original tumors. Notably, solid morphology was associated with shorter PFS, suggesting that organoid growth phenotype may serve as a supplementary indicator of tumor biological behavior in HCC. Given the modest cohort size and the absence of multivariate analysis, these preliminary findings should be interpreted with caution and warrant further large-scale validation.

cancer biology↗

bioRxiv2026

Spore-Based Biocomposite Thermoplastic Polyesters with Enhanced Toughness and Programmable Disintegration

Thermoplastic polyesters are widely used in commodity and high-performance applications due to their tunable and exceptional properties, versatile performance, and increasing relevance in sustainable materials. Integrating biological functionality into these polymers offers a promising route to enhance performance and end-of-life behavior beyond what conventional additives can achieve. Here, we report the generalization of an embedded spore-based engineered living material concept to three representative thermoplastic polyesters; polycaprolactone (PCL), polylactic acid (PLA), and poly(butylene adipate-co-terephthalate) (PBAT). Heat-shock-tolerized Bacillus subtilis spores were compounded with each polyester as a living biofiller via hot melt extrusion. The resulting biocomposite polyesters retained high spore viability (>90%) after extrusion and exhibited improved mechanical performance (up to 41% toughness improvement compared to neat polymers). End-of-life behavior was evaluated in a microbially-limited composting environment, where spore-containing PCL exhibited nearly complete disintegration within five months, corresponding to a [~]7-fold increase in degradation kinetics relative to neat PCL. Finally, 3D printing of biocomposite PCL was demonstrated through fused deposition modeling and direct ink writing methodologies. Together, this work demonstrated the successful extension of spore-based engineered living materials from thermoplastic polyurethane to multiple thermoplastic polyesters. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/707801v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@4eaafaorg.highwire.dtl.DTLVardef@bb17c2org.highwire.dtl.DTLVardef@114e4ceorg.highwire.dtl.DTLVardef@b9bd0c_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

A distinct set of brain areas process prosody--the melody of speech

Human speech carries information beyond the words themselves: pitch, loudness, duration, and pauses--jointly referred to as prosody--emphasize critical words, help group words into phrases, and convey emotional and other socially-relevant information. Using a novel fMRI paradigm, we identify a set of prosody-responsive brain areas and then richly characterize them across 8 experiments (25 experimental conditions; n=51 participants). These areas--located on the lateral temporal surface bilaterally and in the frontal lobe--respond to the presence of prosody in both meaningful and meaningless speech, and are distinct from nearby temporal pitch- and speech-perception areas and from frontal areas sensitive to general cognitive and attentional demands. They are also dissociable from--but show partial overlap with--the language areas and with the area that processes dynamic facial expressions. Thus, prosodic information is processed by a distinct set of brain areas, which may help integrate linguistic meanings with non-verbal communicative signals.

neuroscience↗

bioRxiv2025

Naegleria amoebae seek confinement and crawl persistently through narrow spaces

The "brain-eating amoeba" Naegleria fowleri dwells in ponds where it normally feeds on bacteria, but if it enters the brain it can cause a deadly infection. To establish infection, N. fowleri must migrate through different environments--along olfactory axons, through openings in the cribriform plate, and within brain tissue--yet how it does so remains unknown. As a model for N. fowleri migration within these environments, we examine how its non-pathogenic relative, Naegleria gruberi, navigates environments of distinct geometries. We show that Naegleria uses both actin-rich protrusions and membrane blebs to crawl across or between flat surfaces. We also explore how Naegleria interact with narrow channels and find that, unlike Dictyostelium amoebae that we show frequently disengage from channel interfaces, Naegleria amoebae probe channels until they enter. Once inside, Naegleria crawls quickly (>50 m/min) and unidirectionally over long distances (>1 mm) using only bleb-based motility. We also introduced Naegleria to granular hydrogel matrices that mimic pond sediments and found that cells readily enter and migrate through these three-dimensional matrices using both blebs and lamellar protrusions. Although cells in matrices showed lower persistence at short timescales, longer time scales correlate with increased persistence, suggesting Naegleria cells may retain memory of past orientation. We propose that pond life may select for three behaviors that prime Naegleria for pathogenesis: memory-guided motility that would facilitate exploration of sinus cavities, confinement-seeking ("claustrophilia") that would promote entry into narrow passages along olfactory axons, and persistent bleb-based migration that would allow rapid transit along axons to the brain.

cell biology↗

bioRxiv2025

Copper deficiency disrupts OXPHOS and mitochondrial dynamics through MTCH2-dependent copper trafficking in skeletal muscle

Copper is an essential trace element for mitochondrial respiration and cellular metabolism, yet its physiological role in skeletal muscle remains incompletely understood. Here, we show that skeletal muscle-specific deletion of the high-affinity copper importer Ctr1 (SMKO) in mice causes local copper deficiency, resulting in exercise intolerance, systemic metabolic dysfunction, and hallmarks of mitochondrial myopathy such as ragged-red fibers, lactic acidosis, and aberrant mitochondrial morphology. Mechanistically, copper starvation disrupted the electron transport chain proteome and drove pathological mitochondrial hyperfusion. We identified mitochondrial carrier homolog 2 (MTCH2), an outer mitochondrial membrane protein, as a copper-binding regulator that coordinates mitochondrial copper distribution and morphology. Restoring copper levels via a copper ionophore or AAV-mediated Ctr1 re-expression rescued mitochondrial function and alleviated myopathic features in SMKO. These findings uncover the functional coupling of CTR1 and MTCH2 as a critical mechanistic link between copper homeostasis and mitochondrial remodeling required for skeletal muscle function.

molecular biology↗

bioRxiv2025

The interaction of XPG with TFIIH through p62 and XPD is required for the completion of nucleotide excision repair

Nucleotide excision repair (NER) is the key pathway for the removal of DNA damage induced by UV irradiation and chemotherapeutic reagents. Protein-protein interactions are crucial for the dynamic and coordinated assembly of the proteins involved at DNA lesion. Here we focus on the role of interactions between the multi-subunit helicase/translocase complex TFIIH and the 3 endonuclease XPG. We show that XPG interacts with the p62 and XPD subunits of TFIIH through its long spacer region located in the middle of its split active site. We show the interactions between three acidic regions of XPG with the pleckstrin homology (PH) domain of p62 are of moderate importance for NER, while interactions with XPD are critical for activity. Combining mutations in the p62 and XPD interaction domains leads to additive defects in NER activity. Unexpectedly, we show that these interactions are not required for the recruitment of XPG, but rather for the formation of a catalytically competent NER complex and for triggering the incision 5 to the lesion by ERCC1-XPF. Our studies provide fundamental insights into how interactions between TFIIH and XPG contribute to the NER pathway and more generally how modular protein-protein interactions control each step along the NER reaction coordinate.

biochemistry↗

bioRxiv2025

Mechanical environment afforded by engineered polymer hydrogel critically regulates survival of neural stem cells transplanted in the injured spinal cord via Piezo1-mediated mechanotransduction

Neural stem cell (NSC) transplantation is a promising therapeutic approach for spinal cord repair, but poor graft survival remains a critical challenge. Here, we demonstrate that the mechanical properties of the transplantation microenvironment play a crucial role in NSC survival in the injured spinal cord. While our previously engineered imidazole-poly(organophosphazene) (I-5) hydrogel effectively prevented cavity formation by promoting extracellular matrix remodeling, NSCs transplanted with 10% hydrogel exhibited poor survival. Remarkably, increasing the hydrogel concentration to 16%, which created a 5-fold stiffer matrix, significantly enhanced NSC graft survival and synaptic integration. Using in vitro models with controlled substrate stiffness, we found that NSCs on stiffer substrates displayed enhanced adhesion, complex morphology, and increased viability. Importantly, we identified the mechanosensitive ion channel Piezo1 as the key molecular mediator of these stiffness-dependent behaviors. CRISPR/Cas9-mediated Piezo1 gene editing in NSCs significantly reduced graft survival in vivo when transplanted with 16% hydrogel, confirming that Piezo1-mediated mechanotransduction is essential for NSC survival in the injured spinal cord. Our findings reveal a previously unrecognized mechanism governing graft survival in the injured spinal cord and suggest that optimizing the mechanical properties of biomaterial scaffolds or targeting Piezo1-dependent mechanotransduction could substantially improve outcomes of cell-based therapies for neurological disorders.

neuroscience↗

bioRxiv2024

Scalable Fabrication of a Tough and Recyclable Spore-Bearing Biocomposite Thermoplastic Polyurethane

Thermoplastic polyurethanes (TPUs) are a class of versatile thermoplastic elastomers where most of their products lack a proper recycling strategy or have no end-of-life solutions. To pursue a sustainable end-of-life solution for TPU based products, self-disintegrating biocomposite TPUs have recently been developed by embedding spores of TPU-degrading bacteria into TPUs using melt extrusion. Herein, we improve upon spore-bearing biocomposites and demonstrate industrially-relevant manufacturing conditions for the fabrication of biocomposite TPUs. Spore production was modified to reduce the innate brown color of the resulting materials and, effectively minimize the coloration of biocomposite TPUs. Reduction of FeSO4 in a sporulation media generated white spores without compromising spore productivity, viability, morphology or heat-shock tolerance. Biocomposite TPUs containing white spores displayed a 45% increase in toughness compared to TPUs without spores, while retaining [~]90% spore viability post processing. Furthermore, biocomposite TPU fabrication was demonstrated using a scalable continuous extruder followed by injection molding. Biocomposite TPUs generated by these industry-relevant processes exhibited comparable toughness improvement and spore viability to biocomposite TPU prepared using a lab scale microcompounder, while enhancing productivity by 30-fold. Finally, spore addition improved biocomposite TPUs recyclability, enabling 80% toughness retention after 5 rounds of iterative melt processing. Additionally, no negative effect on the lifespan of the generated TPUs was observed over a duration of 1 year of storage. Overall, this study confirmed that spore-bearing biocomposite TPUs are promising for practical applications, offering an accessible method to enhance toughness and sustainability of commercial TPUs through the incorporation of spore-based living fillers.

bioengineering↗

bioRxiv2024

Detrimental Influence of Arginase-1 in Infiltrating Macrophages on Post-Stroke Functional Recovery and Inflammatory Milieu

Post-stroke inflammation critically influences functional outcomes following ischemic stroke. Arginase-1 (Arg1) is conventionally understood as a marker for anti-inflammatory macrophages, associated with the resolution of inflammation and promotion of tissue repair in various pathological conditions. However, its specific role in post-stroke recovery remains to be elucidated. This study investigates the functional impact of Arg1 expressed in macrophages on post-stroke recovery and inflammatory milieu. We observed a time-dependent increase in Arg1 expression, peaking at 7 days after photothrombotic stroke in mice. Cellular mapping analysis revealed that Arg1 was predominantly expressed in LysM-positive infiltrating macrophages. Using a conditional knockout (cKO) mouse model, we examined the role of Arg1 expressed in infiltrating macrophages. Contrary to its presumed beneficial effects, Arg1 cKO in LysM-positive macrophages significantly improved skilled forelimb motor function recovery after stroke. Mechanistically, Arg1 cKO attenuated fibrotic scar formation, enhanced peri-infarct remyelination, and increased synaptic density while reducing microglial synaptic elimination in the peri-infarct cortex. Gene expression analysis of FACS-sorted microglia revealed decreased TGF-{beta} signaling and pro-inflammatory cytokine activity in peri-infarct microglia from Arg1 cKO animals. In vitro co-culture experiments demonstrated that Arg1 activity in macrophages modulates microglial synaptic phagocytosis, providing evidence for macrophage-microglia interaction. These findings provide new insights into Arg1 function in CNS injury and highlight an interaction between infiltrating macrophages and resident microglia in shaping the post-stroke inflammatory milieu. Our study identifies Arg1 in macrophages as a potential therapeutic target for modulating post-stroke inflammation and improving functional recovery.

neuroscience↗

bioRxiv2024

Linguistic inputs must be syntactically parsable to fully engage the language network

Human language comprehension is remarkably robust to ill-formed inputs (e.g., word transpositions). This robustness has led some to argue that syntactic parsing is largely an illusion, and that incremental comprehension is more heuristic, shallow, and semantics-based than is often assumed. However, the available data are also consistent with the possibility that humans always perform rule-like symbolic parsing and simply deploy error correction mechanisms to reconstruct ill-formed inputs when needed. We put these hypotheses to a new stringent test by examining brain responses to a) stimuli that should pose a challenge for syntactic reconstruction but allow for complex meanings to be built within local contexts through associative/shallow processing (sentences presented in a backward word order), and b) grammatically well-formed but semantically implausible sentences that should impede semantics-based heuristic processing. Using a novel behavioral syntactic reconstruction paradigm, we demonstrate that backward- presented sentences indeed impede the recovery of grammatical structure during incremental comprehension. Critically, these backward-presented stimuli elicit a relatively low response in the language areas, as measured with fMRI. In contrast, semantically implausible but grammatically well-formed sentences elicit a response in the language areas similar in magnitude to naturalistic (plausible) sentences. In other words, the ability to build syntactic structures during incremental language processing is both necessary and sufficient to fully engage the language network. Taken together, these results provide strongest to date support for a generalized reliance of human language comprehension on syntactic parsing. Significance statementWhether language comprehension relies predominantly on structural (syntactic) cues or meaning- related (semantic) cues remains debated. We shed new light on this question by examining the language brain areas responses to stimuli where syntactic and semantic cues are pitted against each other, using fMRI. We find that the language areas respond weakly to stimuli that allow for local semantic composition but cannot be parsed syntactically--as confirmed in a novel behavioral paradigm--and they respond strongly to grammatical but semantically implausible sentences, like the famous Colorless green ideas sleep furiously sentence. These findings challenge accounts of language processing that suggest that syntactic parsing can be foregone in favor of shallow semantic processing.

neuroscience↗

bioRxiv2024

Divergent short-term plasticity creates parallel pathways for computation and behavior in an olfactory circuit

To enable diverse sensory processing and behavior, central circuits use divergent connectivity to create parallel pathways. However, linking subcellular mechanisms to the circuit-level segregation of computation has been challenging. Here, we investigate the generation of parallel processing within a divergent network in the Drosophila olfactory system, where single projection neurons target multiple types of lateral horn neuron (LHN). One LHN type generates sustained responses and adapts divisively to encode temporal odor contrast. The other generates transient responses and adapts subtractively to encode a form of positive temporal prediction error. These coding differences originate from subcellular differences in short-term plasticity in projection neuron axons. Prediction error arises from strongly facilitating synapses, which depend on the presynaptic priming factor Unc13B. The temporal contrast code arises from mildly depressing synapses that engage additional gain control implemented by the Na+/K+ ATPase in the postsynaptic neuron. Each LHN type makes corresponding dynamic contributions to behavioral odor attraction. Subcellular synaptic specialization is a compact and efficient way to generate diverse parallel information streams.

neuroscience↗

bioRxiv2024

Detailed mechanisms for unintended large DNA deletions with CRISPR, base editors, and prime editors

CRISPR-Cas9 nucleases are versatile tools for genetic engineering cells and function by producing targeted double-strand breaks (DSBs) in the DNA sequence. However, the unintended production of large deletions (>100 bp) represents a challenge to the effective application of this genome-editing system. We optimized a long-range amplicon sequencing system and developed a k-mer sequence-alignment algorithm to simultaneously detect small DNA alteration events and large DNA deletions. With this workflow, we determined that CRISPR-Cas9 induced large deletions at varying frequencies in cancer cell lines, stem cells, and primary T cells. With CRISPR interference screening, we determined that end resection and the subsequent TMEJ [DNA polymerase theta-mediated end joining] repair process produce most large deletions. Furthermore, base editors and prime editors also generated large deletions despite employing mutated Cas9 "nickases" that produce single-strand breaks. Our findings reveal an important limitation of current genome-editing tools and identify strategies for mitigating unwanted large deletion events.

genetics↗

bioRxiv2023

Biocomposite Thermoplastic Polyurethanes Containing Evolved Bacterial Spores as Living Fillers to Facilitate Polymer Disintegration

The field of engineered living materials (ELMs) seeks to pair living organisms with synthetic materials to generate biocomposite materials with augmented function since living systems can provide highly-programmable and complex behavior. ELMs have typically been fabricated using techniques in benign aqueous environments, limiting their application. In this work, biocomposite fabrication was demonstrated in which spores from polymer-degrading bacteria were incorporated into a thermoplastic polyurethane (TPU) using high-temperature melt processing. Bacteria were engineered using adaptive laboratory evolution to improve their heat tolerance to ensure nearly complete cell survivability during manufacturing at 135 {degrees}C. Furthermore, the overall tensile properties of spore-filled TPUs were substantially improved, resulting in a significant improvement in toughness. The biocomposites facilitated disintegration in compost in the absence of a microbe-rich environment. Finally, spores retained a programmed function, expressing green fluorescent protein. This research provides a scalable method to fabricate advanced biocomposite materials in industrially-compatible processes.

bioengineering↗