Biology subjects

Yu, K.

Publications and source records attributed to Yu, K..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Transcranial focused ultrasound induces source localizable cortical activation in resting state humans when applied concurrently with transcranial electric stimulation

The effects of transcranial focused ultrasound (tFUS) on the human brain are poorly understood. Currently, the field is at odds with whether tFUS is subthreshold modulating the brains excitability towards other stimuli, producing suprathreshold neural stimulation on its own, or if it even has a spatially specific non-auditory induced affect. Herein, we investigated the ability of tFUS, transcranial direct current stimulation (tDCS) and a novel combination of the two (transcranial electro-acoustic stimulation; tEAS) to evoke cortical target-location specific activity in 27 resting state humans with whole brain electroencephalography recordings. In none of the exogenous event related potentials did tFUS or tDCS result in location-specific activations. However, the co-modulatory combination of tEAS did, providing evidence that tFUS has a location-specific subthreshold modulatory effect. We propose a minimally modified Hodgkin Huxley model that explains our results and provides a unifying framework for the field-wide observed effects (or lack thereof) of tFUS.

neuroscience↗

bioRxiv2025

The anti-retroviral therapy emtricitabine affects skeletal muscle DNA methylation and transcriptome patterns in a male HIV mouse model

BackgroundAlthough antiretroviral therapies (ART) have substantially reduced HIV-associated mortality, the increased lifespan achieved by widespread ART deployment has revealed that HIV infection is linked to an unexplained earlier onset and increased incidence of aging-associated conditions like sarcopenia. Complex syndromes, like sarcopenia, often arise from a combination of genetic and environmental factors, so in this study, we investigated effects of short-term treatment with emtricitabine (2,3-dideoxy-5-fluoro-3-thiacytidine; FTC), an FDA approved ART, on skeletal muscle DNA methylation patterns and transcriptome-wide responses in a male murine model of HIV phenotypic biology (Tg26 mice). MethodsWe treated 6 month old male Tg26 (+/-) mice or wildtype (WT) littermates on a C57BL/6 genetic background with FTC in the drinking water for one month; control groups received drinking water vehicle alone (VEH). Muscle function and body composition were measured longitudinally. Skeletal muscle methylation patterns, transcriptional changes, and histological features were quantified at sacrifice. ResultsAlthough neither gross structural nor functional muscle deficits were observed in this short-term study with ART usage, relative decreases in muscle endurance measured by hang time over the study were 2-fold more severe in the Tg26 as compared to WT mice (p=0.0453), and markers of myogenic cell maturation (Myf5, Myf6) were disrupted in the Tg26 HIV model as compared to WT littermates in a manner exacerbated by FTC treatment. Fat mass, measured by DXA, also tended (p=0.085) to be uniquely increased by FTC treatment in the Tg26 mice over the study. Differential methylation patterns and pathway enrichment data suggested that the presence of an HIV phenotype and exposure to an ART regimen altered the methylation status in skeletal muscle genes such as Camk2B, Pcolce2 and Lima1 in a manner consistent with promoting eventual functional impairment in muscle. Additionally, RNAseq revealed differential gene expression profiles and key regulatory pathways including cellular differentiation, regulation of lipid metabolism, and neuroactive ligand-receptor interactions. Lipodystrophy-related genes including LEP, ADIPOQ and PPAR involved in fat distribution and metabolism along with skeletal genes related to regulation of muscle strength were affected by the presence of an HIV phenotype and ART treatment. ConclusionsThe current study provides insights into mechanisms by which a clinically relevant ART may influence DNA methylation and transcriptome changes in skeletal muscle in the context of HIV biology. The differentially regulated pathways suggest novel targets for understanding, and eventually abrogating, the harmful effects of long-term ART use in PLWH on skeletal muscle mass and function.

cell biology↗

bioRxiv2025

Nuclear Packing Sets Fluidity Along the Epithelial to Mesenchymal Spectrum

Investigations of jamming in cancer have produced numerous phase diagrams intending to map fluidity across the epithelial-to-mesenchymal transition (EMT). Here, we use coalescence of homotypic and heterotypic multicellular spheroids to examine and carefully probe these phase spaces. Small changes in cellular EMT status result in full traversal of the solid-to-fluid continuum. We propose that stiff nuclei impede cell motion and spheroid coalescence and find that by softening nuclei, fluidization of an otherwise solid-like system occurs. Changes in fluidity during coalescence is fully captured by static cellular properties, such as internuclear spacing and nuclear shape, that can be assessed in individual non-interacting spheroids. We combine these quantities into an effective nuclear packing metric that depends on nuclear occupancy and nuclear elongation. Together, these findings reveal that nuclear morphology and packing act as important indicators and determinants of fluidity.

biophysics↗

bioRxiv2025

Global Mapping of Combinatorial Chromatin Regulatory Events Using Hi-Plex CUT&Tag

Epigenetic modulators, transcription factors, and chromatin-associated proteins collaboratively regulate essential genomic functions, such as transcription, repression, and DNA damage repair. However, the intricate cross-talk or the interaction between these chromatin regulatory factors (CRFs) remains poorly understood, largely due to limitations in experimental methods, which traditionally interrogate the genomic locations of only one CRF. Although the latest methods can study multiple CRFs simultaneously, they cannot examine the interaction between these factors. Inferring biological interactions often requires integrating data from multiple experiments, which can be labor-intensive and imprecise since the measurement is not from the same DNA molecule. To address these challenges, we developed Hi-Plex CUT&Tag, an advanced technology that enables the robust detection of co-localization events across over 600 pairs of CRFs using 36 barcoded monoclonal antibodies (mAbs), while minimizing background signals and cross-contamination. Hi-Plex CUT&Tag facilitates comprehensive pairwise analysis of epigenetic modifiers, including histone post-translational modifications (PTMs), writers, and transcription factors (TFs). Each Tn5 tagmentation fragment provides detailed insights, capturing the identities of two co-localized events, the underlying genomic sequences, and the molecular distance between them. For the first time, numerous novel bivalent events, epigenetic-context-dependent transcriptional regulation, and specific chromatin mark combinations with significant impacts on gene regulation can be detected in a single experiment. Furthermore, single-cell Hi-Plex CUT&Tag enables the analysis of synergistic interactions between CRF pairs at the single-cell level, providing unprecedented resolution for studying chromatin dynamics.

genetics↗

bioRxiv2025

Theta and gamma transcranial alternating current stimulation modulate Mandarin consonant and lexical tone perception

A theta/gamma oscillatory neural mechanism has been postulated to explain the auditory sampling of hierarchical syllable-phoneme structure with corresponding speech rates or linguistic hierarchies (theta for syllable and gamma for phoneme). Yet, whether such a mechanism is generalizable to Mandarin Chinese, a language that both has suprasegmental phonemes in the form of lexical tones and contains more monosyllabic words, which may lead to higher reliance on either phonemic-level or syllabic-level perceptual representations, is unclear. In this study, we applied transcranial electric stimulation with either theta or gamma alternating currents (tACS) to bilateral auditory cortices in healthy Mandarin-speaking participants during a consonant or tone identification task in quiet or noisy environments. Results showed that theta tACS impaired consonant identification in quiet, specifically, and generally prolonged reaction times across tasks and environments. Gamma tACS, however, only delayed tone identification in quiet. Besides, both theta and gamma tACS modulated perceptual decision-making parameters, leading to increased boundary thresholds (cautiousness of decision) and altered response biases in the perceptual decision of both consonants and tones, as evidenced by the hierarchical drift-diffusion model (HDDM). These findings indicate that theta oscillations causally support the perception of Mandarin syllables, with consonants and lexical tones presumably embedded in syllable-level representations, regardless of task difficulty. Gamma activity, however, is presumably engaged in supporting fast-changing and fine-grained acoustic features in a modulatory manner. Significance StatementHow the brain samples speech features for perception is a key question in language neuroscience. Previous research has shown that theta and gamma brain activity support the perception of suprasegmental syllables and segmental phonemes, corresponding to their length or linguistic hierarchy. However, for Mandarin, the existence of suprasegmental phonemes (lexical tones) and the large number of monosyllabic words can either lead to higher reliance on gamma oscillations for phoneme perception, or higher dependence on theta oscillations for holistic syllable integration. With the combination of brain stimulation to selectively modulate theta/gamma auditory activity and phoneme identification tasks, this study reveals a causal role of theta activity in supporting holistic syllable-based Mandarin phoneme perception, yet gamma engagement is modulatory.

neuroscience↗

bioRxiv2025

A Novel Drosophila Model of Cancer Cachexia Reveals Conserved Jak/Stat Dependent Glucagon-like Akh Activation as a Driver of Metabolic Reprogramming and Systemic Wasting

Cancer-associated cachexia is a systemic wasting syndrome with no effective therapies, and results in millions of deaths annually. Here, we establish a novel Drosophila model of cancer cachexia using overexpression of Hipk and constitutively active Sik3 in larval epithelial tissue. Tumor-bearing larvae has significant muscle and fat body wasting, together with elevated carbohydrates and lipolysis. Mechanistically, tumors secrete Unpaired ligands that activate Jak/Stat signaling in corpora cardiaca (cc) cells, inducing the expression and protein levels of glucagon-like hormone Adipokinetic hormone (Akh). Elevated Akh, together with the lipase Brummer (Bmm), drives the aforementioned systemic metabolic reprogramming and tissue catabolism. In conclusion, this study identifies a conserved tumor-host Upd-JAK/STAT-Akh signaling axis that contributes to organ wasting.

cancer biology↗

bioRxiv2025

A synaptic mechanism for encoding the learned value of action-derived safety

Motivated behavior is often framed in terms of biologically grounded outcomes, such as food or threat. Yet many motivated actions, like the pursuit of safety or agency, depend on outcomes that lack explicit sensory value and must instead be inferred from experience. Here, we identify a thalamostriatal circuit mechanism by which such internally constructed outcomes acquire motivational value. In mice performing an active avoidance task, neurons in the paraventricular thalamus (PVT) projecting to the nucleus accumbens (NAc) develop a safety-encoding signal that emerges following successful avoidance. This signal is experience-dependent and value-sensitive, diminishing upon devaluation of the instrumental contingency. Selective silencing of the PVT[->]NAc projection at safety onset disrupts avoidance persistence without impairing action-outcome learning, as confirmed by computational modeling of value updating based on prediction error. Mechanistically, PVT input recruits cholinergic interneurons (CINs) to modulate dopamine release and this influence depends on synaptic potentiation mediated by GluA2-lacking AMPA receptor insertion at PVT-CIN synapses. Disrupting this plasticity selectively impairs the avoidance response by blunting the motivational value of safety without affecting acquisition. These findings reveal how thalamic circuits assign value to abstract, internal outcomes, providing a framework for understanding how goals like safety are inferred, stabilized, and rendered behaviorally effective.

neuroscience↗

bioRxiv2025

CloneCoordinate: Open-source software for collaborative DNA construction

Custom DNA constructs have never been more common or important in the life sciences. Many researchers therefore devote substantial time and effort to molecular cloning, aided by abundant computer-aided design tools. However, support for managing and documenting the construction process, and for effectively handling and reducing the frequency of setbacks, is lacking. To address this need, we developed CloneCoordinate, a free, open-source electronic laboratory notebook specifically designed for cloning and fully implemented in Google Sheets. By maintaining a real-time, automatically prioritized task list, a uniform physical sample inventory, and standardized data structures, CloneCoordinate enables productive, collaborative cloning for individuals or teams. We demonstrate how the information captured by CloneCoordinate can be leveraged to troubleshoot assembly problems and provide data-driven insights into cloning efficiency. CloneCoordinate offers a new and uniquely accessible model for how to carry out, and iteratively improve on, real-world DNA assembly.

synthetic biology↗

bioRxiv2025

Spatial and temporal scale-dependent feedbacks govern dynamics of biocrusts in drylands

Biota could be ecosystem engineers in generating an intrinsic heterogeneous landscape through scale-dependent feedbacks. Thereby, they can form resource enriched patchiness or islands of fertility, comprising of self-organizing spatial patterns. Research so far has largely focused on the self-organized spatial patterns of plant communities in drylands. It, however, remains unclear whether and how biocrusts having distinct morphology and life history from plant communities could self-organize themselves and form unique spatial patterns. Here we conducted field observations of biocrusts across successional stages and employed a probabilistic Cellular Automaton (CA) model to investigate the distinct self-organized spatial patterns exhibited by mosaic patches of mosses and lichens with different patch size distributions (PSDs). Our study demonstrates that short-range positive feedbacks initially promote the development of patches, featured with a heavy-tailed PSD, while long-range negative feedbacks subsequently curtail further expansion of big patches, thereby establishing a characteristic patch scale with regular PSDs. Strikingly, only lichens reverted back to the heavy-tailed PSD in the late succession stage, presumably implying self-organized critical fragmentation of lichen patches. Field measurements of biocrust performance at the center and edge of patches of varying sizes along succession stages further support the classic scale-dependent feedback mechanism for Turing pattern formation. Collectively, our results clearly demonstrate the capability of the biocrust communities to self-organize themselves to form distinct spatial patterns governed by the spatial and temporal scale-dependent feedbacks, potentially impacting dryland ecosystem functions and resilience. Significance StatementAn intriguing phenomenon is the capability of biota to form striking self-organized spatial patterns. Biocrusts serve as the soils skin and have different morphology and life history as compared to plant communities. We investigated these distinct self-organized spatial patterns exhibited by mosaic patches of mosses and lichens across succession stages through field surveys and a probabilistic Cellular Automaton (CA) model. Our results provide empirical evidence that biocrusts act as ecosystem engineers, forming self-organized spatial patterns. Simulations and field measurements of biocrust performance elucidate the mechanism of spatial and temporal scale-dependent feedbacks in governing biocrust spatial pattern formation. This self-organizing ability of biocrusts holds significant implications for ecosystem functions and the resilience of dryland ecosystems.

ecology↗

bioRxiv2025

Microbially-mediated halogenation and dehalogenation cycling of organohalides in the ocean

Microbially mediated organohalide cycling in the ocean has profound implications for global element cycles and climate, but the phylogeny, coding potential, and distribution of the halogenation-dehalogenation cycling microorganisms remain unknown. Here, we construct an organohalide-cycling database (HaloCycDB) to explore the global atlas of halogenation-dehalogenation cycling genes and microorganisms in the ocean from 1,473 marine metagenomes. FlaHase and HyDase/RDase as predominant halogenase- and dehalogenase-encoding genes account for 80.24% of all potential organohalide-cycling activities. We identify 80.91% RDase and 91.35% RDase-containing prokaryotes as unknown organohalide-cycling genes and microorganisms, respectively, which greatly expand the diversity of dehalogenation phylogeny and coding potential. Further integration of microbial cultivation with protein structure prediction and molecular docking elucidates 4 unique "microorganism-enzyme-organohalide" patterns for organohalide dehalogenation in the ocean. Our results provide the first insight into microbial halogenation-dehalogenation cycling of organohalides and associated yet-to-be-explored resources in the ocean.

ecology↗

bioRxiv2025

In C57Bl6 Mice, Obesity and Subsequent Weight Loss Negatively Affected the Skeleton and Shifted the Cortical Bone Metabolome

Obesity and calorie restriction each negatively affect skeletal health. Despite the negative effects of weight loss on the skeleton, obese patients are advised to lose weight via calorie restriction. Additionally, obesity and weight loss individually alter both whole-body and local metabolism. Little is known about bone quality and changes to the cortical metabolome following calorie restriction in obese preclinical models. We hypothesized that caloric restriction would worsen bone quality in obese mice by shifting the cortical bone metabolome. To induce obesity, 8-week-old male and female C57BL6/J mice received 60% high-fat diet for 12 weeks. From 20 to 30 weeks of age, mice either remained obese or lost weight through 30% caloric restriction. Control animals received a 10% low-fat diet. Bodyweight and fat mass were increased by obesity and decreased with calorie restriction. Similarly, glucose and insulin tolerance were worsened with obesity but improved by weight loss. Compared to obesity, calorie restriction elicited more bone loss in both cortical and trabecular compartments. Weight loss also reduced bone formation. Both obesity and subsequent calorie restriction altered the cortical bone metabolome in a sex-dependent manner. Metabolic pathways altered with diet generally mapped to amino acid or fatty acid metabolism. In males, weight loss was associated with a downregulation of pathways related to tryptophan, tyrosine, ubiquinone, and fatty acids. In females, calorie restriction downregulated taurine and hypotaurine metabolism but upregulated pyrimidine metabolism, nicotinate and nicotinamide metabolism, and pantothenate and CoA biosynthesis. Our findings highlight the negative effects of obesity and subsequent caloric restriction on the skeleton. Despite improvements in components of systemic metabolism, caloric restriction in obese preclinical models did not restore bone morphology or the cortical metabolome to control conditions.

cell biology↗

bioRxiv2025

EZHIP boosts neuronal-like synaptic gene programs and depresses polyamine metabolism

It is currently understood that the characteristic loss of the repressive histone mark H3K27me3 in PFA ependymoma and diffuse midline glioma (DMG) are caused by complementary mechanisms mediated by EZHIP and the oncohistone H3K27M, respectively. To support the complementarity of these mechanisms, rare H3K27M-negative DMGs express EZHIP. Interestingly, EZHIP is one of the few genes recurrently mutated in PFA. The significance of EZHIP mutations in PFA, and whether EZHIP has wider functions in addition to repression of H3K27me3 deposition, are not known. Here, we investigated the mutational landscape of EZHIP in pediatric brain tumors. We found that EZHIP mutations occur not only in PFA, but also in rare medulloblastoma and pediatric high-grade glioma (HGG), including in H3K27-positive DMG. Contrary to current expectations, we show that mutant EZHIP is expressed in H3K27M-positive DMG. All the EZHIP-mutated HGG cases also have EGFR mutations. Further, we pursued better understanding of the function of EZHIP by expressing it in human-derived neural models. Our transcriptomic analyses indicate that EZHIP expression potentiates neuronal-like gene programs associated with synaptic function. Metabolomics data indicate that EZHIP leads to repression of methionine and polyamine metabolism, suggesting links between metabolic and epigenetic changes that are observed in PFA. Collectively, our results expand the repertoire of tumor types known to harbor EZHIP mutations and shed light on EZHIP-dependent metabolic and transcriptional programs in relevant neural models.

cancer biology↗

bioRxiv2025

GenVS TBDB: An Open AI-Generated andVirtual Screened Small-Molecule Database for Tuberculosis Drug Discovery

Tuberculosis (TB) remains a leading global health threat, with over 10 million new cases and 1.25 million deaths reported in 2023. Current TB therapies rely on a limited drug repertoire and prolonged treatment courses that have changed little in four decades. Here, we present GenVS-TBDB, a target-aware AI-generated and virtual-screened small-molecule database, which expands the chemical space against Mycobacterium tuberculosis (M.tb) essential proteins. We first identified 460 probable small-molecule binding pockets across 377 essential M.tb proteins by integrating multiple sources. Then, by leveraging the target-aware molecule generative model, over 1.2 million novel small molecules tailored to these pockets were produced. The key physicochemical properties were computed for all compounds to ensure medicinal chemistry tractability. These compounds were also evaluated using molecular docking and anti-TB specific graph neural network model, yielding binding propensity ranking and whole-cell activity prioritization for each target. To substantiate the integrated AI-driven workflow for anti-TB discovery, 30 compounds were obtained, including 22 AI-designed molecules synthesized de novo and 8 commercially available analogs. In validation, 2 synthesized compounds demonstrated significant thermal stabilization of FtsZ, confirming target engagement. 6 compounds exhibited cellular inhibition below 50 {micro}M, the most potent at 12 {micro}M. Furthermore, GDI-11785 showed binding to the cell wall biosynthesis pathway with 35 {micro}M cellular activity, establishing a promising starting point for tuberculosis drug discovery. Our findings contribute a significant library of bioactive molecules which may hasten the preliminary phase of tuberculosis drug discovery. The GenVS-TBDB small library is publicly accessible and can be downloaded freely at https://datascience.ghddi.org/database/view.

pharmacology and toxicology↗

bioRxiv2025

Improving Targeting Specificity of Transcranial Focused Ultrasound in Humans Using a Random Array Transducer: A k-Wave Simulation Study

Transcranial focused ultrasound (tFUS) has emerged as a promising non-invasive modality for precision neuromodulation. However, the heterogeneous acoustic properties of the skull often induce phase aberrations that shift the ultrasound focus and compromise energy delivery. In this study, we developed and validated a phase-reversal based aberration correction method to enhance the targeting specificity of tFUS using a 128-element random array ultrasound transducer. Individual head models were constructed from T1-weighted magnetic resonance (MR) images and corresponding pseudo-computed tomography (pCT) data to accurately represent subject-specific skull geometries and the targeted left V5 (V5L) region. Acoustic simulations were conducted with the k-Wave toolbox by first acquiring free-field pressure waveforms and then recording the aberrated waveforms in the presence of the skull. The phase differences between these conditions were used to compute corrective delays for each transducer element. Quantitative evaluation using metrics such as focal overlap with the target region, axial focal positioning, and the delivered ultrasound energy demonstrated significant improvements: the overlap volume increased by 98.70%, mean axial positioning errors were reduced by up to 14.36%, and energy delivery to the target improved by 17.58%. We further demonstrated that the proposed approach outperforms the conventional ray-tracing methods. The results show that phase-reversal based aberration correction markedly increases the spatial targeting accuracy of tFUS and enhances the efficiency of focused ultrasound energy deposition for the customized random array transducer, paving a way for effective and personalized non-invasive neuromodulation therapies.

bioengineering↗

bioRxiv2025

Cultivating Future Materials: Artificial Symbiosis for Bulk Production of Bacterial Cellulose Composites

Symbiotic relationships between micro-organisms are the basis of all global ecosystems. Here we extrapolate this concept for novel material fabrication by creating artificial symbiotic relationships between species that are usually not grown synergistically in nature. Specifically, we combine the cellulose-producing bacterium Komagataeibacter hansenii and the green microalga Chlamydomonas reinhardtii to obtain bulk growth of bacterial cellulose. Usually, bacterial cellulose is produced as floating pellicles at the air-liquid interface of the growing media, because free oxygen, together with the nutrients in the culture medium, is required for the bacteria to synthesise the cellulose fibres. In the co-culture, bacterial cellulose production can be achieved in bulk beyond the restriction of the liquid/air interface as the motile microalgae act as oxygen-generating sites within the culture medium. In exchange, the highly porous and mechanically robust scaffold provided by the cellulose allows the algal community to form a healthy biofilm, which can reach several centimetres thick. We demonstrate that our growing platform allows the simultaneous production of bulk bacterial cellulose in static incubation conditions, taking up an arbitrary and yet tunable 3D shape, dependent on the geometry of the culture vessel and with a relatively high biomass output.

microbiology↗

bioRxiv2025

Construction of Complete Telomere-to-Telomere Genome Assembly of the Rabbit Using Haploid Embryonic Stem Cells

The rabbit owns commercial importance in meat and fur production, and also has long served as a valuable animal model in biomedical research. Yet, the complete assembly of a high-quality rabbit reference genome has not been established. Here, we present a telomere-to-telomere (T2T) genome assembly of the New Zealand White (NZW) rabbit, the most complete and accurate rabbit genome to date. Using a haploid embryonic stem cells (haESCs) to overcame the challenges of homologous sequence interference and structural variation, we generate a genome with a contig N50 of 137.71 Mb, anchoring all chromosomes with only three gaps, through integrating long-read sequencing (PacBio HiFi, Oxford Nanopore), Hi-C, and Illumina data. Quality assessments reveal near-complete coverage of the BUSCO mammalian gene set, with 99.61% completeness. Notably, this complete assembly allowed for the first comprehensive annotation of the rabbit immunoglobulin loci and major histocompatibility complex region, which were previously unresolved in earlier genome versions. The NZW-T2T assembly based on haESCs not only provides a critical resource for advancing rabbit-based research, but also set a new benchmark for de novo genome assembly for other animals with complex genome.

genomics↗

bioRxiv2025

A robust platform streamlining aromatic noncanonical amino acid biosynthesis and genetic code expansion in E. coli

Genetic code expansion has significantly enhanced the diversity and functionality of proteins in the biological world, leading to a wide range of applications in catalysis, biology, and medicine. Despite the extraordinary advances in genetic code expansion over the past years, the availability and cost of noncanonical amino acids (ncAAs) remain one of the major obstacles, particularly for large-scale industrial production. In situ biosynthesis of ncAAs from commercially available precursors offers a promising solution to this challenge, yet only a few biosynthetic pathways for specific amino acids have been reported to date. To address this gap, we present a robust platform that couples the biosynthesis of aromatic amino acids with genetic code expansion in E. coli, enabling the production of proteins and peptides containing incorporated ncAAs. Forty amino acids with diverse functional groups were synthesized from aryl aldehydes by a biosynthetic pathway comprising two heterologously expressed enzymes and one endogenous enzyme. Nineteen of these amino acids were successfully incorporated into superfolder GFP (sfGFP) using three classic orthogonal translation systems. The platforms versatility was further demonstrated by the production of macrocyclic peptides and antibodies containing functional ncAAs, such as para-azidophenylalanine and para-boronophenylalanine. We envision that the simplicity, efficiency, compatibility, and broad applicability of this biosynthetic pathway and the platform will greatly facilitate the production of peptides, enzymes, and antibodies containing ncAAs, thereby accelerating their use in various applications. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC="FIGDIR/small/631627v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@8a6d2eorg.highwire.dtl.DTLVardef@5f8b9org.highwire.dtl.DTLVardef@c514aorg.highwire.dtl.DTLVardef@acd66d_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

Stimulus-driven cerebrospinal fluid dynamics is impaired in glaucoma patients

Cerebrospinal fluid (CSF) dynamics, driven by sensory stimulation-induced neuronal activity, is crucial for maintaining homeostasis and clearing metabolic waste. However, it remains unclear whether such CSF flow is impaired in age-related neurodegenerative diseases of the visual system. This study addresses this gap by examining CSF flow during visual stimulation in glaucoma patients and healthy older adults using functional magnetic resonance imaging. The findings reveal that in glaucoma, CSF inflow becomes decoupled from visually evoked blood-oxygenation-level-dependent (BOLD) response. Furthermore, stimulus-locked CSF patterns, characterized by decreases following stimulus onset and increases after offset, diminish as glaucoma severity worsens. Mediation analysis suggests that this flattened CSF pattern is driven by a flatter BOLD slope, resulting in a shallower CSF trough and a reduced rebound. These findings unveil a novel pathophysiological mechanism underlying disrupted stimulation-driven CSF dynamics in glaucoma and highlight potential in vivo biomarkers for monitoring CSF in the glaucomatous brain.

neuroscience↗