Biology subjects

Yamada, K.

Publications and source records attributed to Yamada, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Melanin-concentrating hormone inhibits PVN oxytocin neurons through a barium-sensitive inwardly rectifying potassium channels and MCH-neuron ablation alters pup-directed aggression

Interactions between melanin-concentrating hormone (MCH) neurons and oxytocin neurons are crucial for parental care. Whole-cell patch-clamp recordings demonstrated that MCH inhibits paraventricular hypothalamic nucleus (PVN)-oxytocin neurons through activation of barium-sensitive inwardly rectifying potassium channels, potentially G-protein coupled inwardly rectifying potassium channels, and pup-directed aggression was positively related to loss of MCH neurons. Our findings offer a glimpse into the neural mechanisms underlying the evolutionary regulation of offspring caregiving and abuse in males.

neuroscience↗

bioRxiv2026

Distinct cognitive and structural correlates of pain extent and central sensitization symptoms in older women and men with chronic pain

Chronic pain in later life may be accompanied by alterations in brain structure and cognition, but whether pain extent and central sensitization symptoms identify distinct brain-behavior patterns remains unclear. We examined associations of pain extent and central sensitization symptoms, assessed using the 9-item Central Sensitization Inventory (CSI-9), with regional gray matter volume and cognitive function in community-dwelling older adults. This cross-sectional study included 272 participants with chronic pain from the Bunkyo Health Study. Participants were classified as having single-site or multisite pain and by CSI-9 score as having lower or higher scores, with 12 or higher defining the higher group. Regional gray matter volume was quantified using 0.3-Tesla magnetic resonance imaging, and cognition was assessed using the Trail Making Test Part B (TMT-B), processing speed, and global and domain-specific measures. Pain extent and CSI-9 group interacted for TMT-B performance, with the longest completion time in participants with single-site pain and a higher CSI-9 score. No other cognitive outcome remained significant after correction for multiple testing. In categorical analyses, the higher CSI-9 group had smaller volumes in the right middle frontal gyrus, bilateral anterior cingulate cortex, right insula, right hippocampus, and bilateral amygdala, whereas pain extent and the interaction were not associated with regional volume. In a contextual comparison, only the single-site/higher CSI-9 group showed slower TMT-B performance than participants with no pain. Pain extent and central sensitization symptoms may represent partly distinct dimensions of chronic pain, although the small single-site/higher CSI-9 group and attenuation in several sensitivity analyses warrant caution. Significance StatementChronic pain is often described by where it hurts, but location alone may miss important differences between patients. In older adults, pain extent and symptoms measured by the 9-item Central Sensitization Inventory captured partly different aspects of chronic pain. Participants with pain at one site and a higher CSI-9 score performed most slowly on a task requiring attention and mental flexibility, whereas differences in regional brain structure were related mainly to CSI-9 score rather than pain extent. These findings support a multidimensional approach to chronic pain and may inform future research on cognitive vulnerability and brain health across pain conditions. Graphical Abstract Text O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/742487v2_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@8f6b84org.highwire.dtl.DTLVardef@1dbe805org.highwire.dtl.DTLVardef@5ddec3org.highwire.dtl.DTLVardef@cbff7a_HPS_FORMAT_FIGEXP M_FIG C_FIG Among older adults with chronic pain, pain extent and CSI-9 score captured different aspects of vulnerability. Slower performance on a task requiring attention and cognitive flexibility was concentrated in those with single-site pain and higher CSI-9 scores, whereas regional brain-volume differences tracked CSI-9 category more broadly.

neuroscience↗

bioRxiv2026

Multidimensional characterization of the physiological and behavioral effects of TCB-2 in mice

Background and PurposeSerotonergic psychedelics affect behavior and physiology, but the relationships among these effects remain poorly understood. In rodents, the head-twitch response is used as a measure of psychedelic-like activity, yet it does not capture changes in physiological state or the performance of learned behaviors. Here, we investigated the acute effects of the 5-HT2A receptor agonist TCB-2 across several behavioral and physiological measures and examined how these effects were modified by pretreatment with the 5-HT2A receptor antagonist volinanserin. Experimental ApproachMice were tested in head-fixed and freely moving conditions. During a learned auditory trace-conditioning task, we measured licking, pupil area, eye position, and blinking. We measured locomotor activity in an open field and quantified head-twitch responses using a DeepLabCut-based method. To examine the contribution of 5-HT2A receptors, mice were pretreated with the 5-HT2A receptor antagonist volinanserin. Key ResultsTCB-2 caused pupil constriction without detectable changes in eye position or blinking when administered alone. TCB-2 also reduced licking at the highest dose, but the cue-locked temporal pattern of licking remained evident. In freely moving mice, TCB-2 reduced locomotor activity and produced a dose-dependent increase in head-twitch responses. Volinanserin partially attenuated TCB-2-induced pupil constriction and reduced head-twitch responses under some conditions, but it did not consistently prevent the other effects of TCB-2. Conclusions and ImplicationsTCB-2 produced distinct effects across physiological and behavioral measures rather than a uniform disruption of behavioral function. Pronounced pupil constriction and head-twitch responses occurred without detectable changes in eye position or blinking, while the temporal organization of conditioned licking was retained despite a reduction in its magnitude. The incomplete and variable effects of volinanserin preclude definitive conclusions about the receptor mechanisms underlying each response. Combining automated head-twitch detection with physiological and task-related measurements provides a broader framework for comparing the pharmacological profiles of serotonergic compounds. What is already knownO_LIClassical psychedelics produce characteristic effects primarily through serotonin 5-HT2A receptor activation. C_LIO_LIHead-twitch responses capture only one dimension of psychedelic-like drug action. C_LI What this study addsO_LITCB-2 reduced locomotion and licking while preserving the cue-locked pattern of conditioned licking. C_LIO_LIPupil constriction occurred without detectable changes in eye position or blinking. C_LI Clinical significanceO_LIMultidimensional phenotyping can distinguish the physiological and behavioral profiles of serotonergic compounds. C_LIO_LIComplementary measures may improve preclinical evaluation of emerging serotonergic therapeutics. C_LI

pharmacology and toxicology↗

bioRxiv2026

KCNQ2/3 Regulates the Synaptic Remodeling Associated with Drug Seeking in Addiction

Drug-seeking behavior during withdrawal represents a critical obstacle to addiction treatment. In the nucleus accumbens, hyperactive dopamine D1 receptor-expressing medium spiny neurons (D1R-MSNs) promote cocaine-seeking through aberrant synaptic remodeling, including synapse formation and calcium-permeable AMPA receptor (CP-AMPAR) insertion. However, the intermediate molecular control mechanism remains unclear. We identified KCNQ2/3 potassium channels as key regulators of synaptic pathology during withdrawal. Cocaine-conditioned mice showed increased spine density, enhanced surface CP-AMPAR, and elevated neuronal activity 14 days after withdrawal. These phenotypes were reversed by repeated administration of KCNQ2/3 openers or D1R-MSN-specific expression of constitutively active KCNQ2. Functional restoration of KCNQ2/3 suppressed cocaine-seeking behavior and normalized D1R-MSN excitability. These findings suggest that sustained KCNQ2/3 deactivation drives synaptic remodeling during withdrawal, while channel activation offers a potential therapeutic strategy. Furthermore, the results position KCNQ2/3 as a master regulator of drug-seeking behavior and channel activation in D1R-MSNs as a logical target for relapse prevention in addiction.

neuroscience↗

bioRxiv2026

Scalable platform for cellular and biochemical screening of combinatorial small-molecule libraries in droplets

A new pattern of hit discovery is emerging with the rise of chemocentric modalities, such as chemical induced proximity (CIP). Synthesis and functional screening of dynamic, purpose-built libraries, such as E3 ligase biased libraries for targeted protein degradation (TPD), is redefining the druggable landscape. However, this new paradigm arguably lies beyond the remit of conventional screening methods which have been optimized for static, diversity-oriented libraries. To address this gap, we developed microfluidic compound screening in droplets (MicDrop), a scalable platform where purpose-built DNA-encoded one-bead one-compound library members are individually tested at high concentrations in pico-liter sized droplets for either biochemical or cellular function. A proof-of-concept CRBN library demonstrated the robustness of the workflow through an IKZF3 degradation screen which discovered an unexpected succinimide-based IKZF3 degrader, while reproducing the relative potency ranking of reference compounds. Screening of a prospective VHL library for CDO1 recruitment and degradation demonstrated that orthogonal assays gave an informative consensus hit list and an actionable machine-learning (ML) recruitment model. These findings establish a blueprint for intentional discovery of chemical inducers of proximity, while producing reliable data to accelerate ML-based design-make-test-analyze (DMTA) cycles in pursuit of new therapeutics. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/730915v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@12de3cborg.highwire.dtl.DTLVardef@1c6618dorg.highwire.dtl.DTLVardef@12ea42eorg.highwire.dtl.DTLVardef@11cea77_HPS_FORMAT_FIGEXP M_FIG C_FIG

Cell Biology↗

bioRxiv2026

Fully Modified SpyCas9 Guide RNAs Enable Robust Genome Editing In Cells and In Vivo

Precision engineering of CRISPR/Cas9 components has advanced genome editing toward therapeutic applications. Completely chemically stabilized guide RNAs (gRNAs) have the potential to improve in vivo editing efficacy while enabling greater flexibility in delivery strategies. However, previous generations of fully modified guides have been associated with reduced Cas9 activity. Here, we employed an iterative, structure-guided optimization strategy to systematically introduce chemical modifications at each position of SpyCas9 gRNAs. Extending beyond commonly used nucleotide modifications, we incorporated 2-amino-RNA, 4-thio-RNA, and extended nucleic acid (exNA) to generate gRNA designs in which 90-100% of the nucleotides are sugar- or backbone-modified. Although certain modification patterns exhibit sequence-dependent variability, we have established a growing repertoire of guides that consistently maintain or enhance editing efficacy when applied both in vitro and in vivo. Collectively, our heavily and fully modified gRNAs hold potential for applications in nuclease editing, base editing, and other genome editing tools. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/725424v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1118f08org.highwire.dtl.DTLVardef@1c57069org.highwire.dtl.DTLVardef@1572148org.highwire.dtl.DTLVardef@14a111e_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

BRCA2 loss triggers a downward spiral of genomic instability via ROS-dependent metabolic collapse

BRCA2 plays a central role in maintaining genome integrity through homologous recombination and replication-fork protection, yet the compensatory networks sustaining BRCA2-deficient cells remain unclear. Here we show BRCA2 enforces a homeostatic mechanism aligning mitochondrial respiration with DNA repair capacity in both cancer and non-cancer contexts. Genome-wide CRISPR screening identified glutathione metabolism and base-excision repair as the key compensatory networks sustaining BRCA2-deficient cells by detoxifying mitochondria-derived reactive oxygen species. BRCA2 loss provokes an acute mitochondrial ROS surge, causing 8-oxoguanine accumulation and a systemic metabolic crisis marked by NAD+ and glutathione depletion. PARP inhibitor targets DNA replication vulnerabilities, increasing the cellular requirement for BRCA2. The resulting oxidative burden primes cells for TP53-dependent apoptosis in G1 during olaparib treatment, which extends cytotoxicity beyond canonical S-phase stress. These findings indicate BRCA2 prevents metabolic flux from outpacing repair capacity, providing a rationale for combining PARP inhibition with redox modulation to enhance efficacy and overcome resistance. HighlightsO_LIAcute BRCA2 loss induces ROS and mitochondrial dysfunction creating a metabolic scar C_LIO_LIOxidative lesions drive PARP hyperactivation and precipitate a cellular NAD crisis C_LIO_LIPARP inhibitors provoke TP53-dependent apoptosis in G1 beyond replication stress in S phase C_LIO_LIGlutathione deficiency exacerbates bone marrow failure under BRCA2 depletion C_LIO_LIBRCA2 tightly couples mitochondrial redox homeostasis to genomic maintenance C_LI

cell biology↗

bioRxiv2026

Circadian Regulation of Taste Sensitivity in Human and Rat Active Periods

Most organisms exhibit endogenous 24-h rhythms that align physiology and behavior with the time of day; however, whether taste sensitivity oscillates in a circadian manner remains unclear, limiting our understanding of its role in feeding behavior. Here, we show that sensitivity to sweet and bitter tastes exhibits circadian modulation, peaking during the active period: daytime in humans and the dark phase in nocturnal rats. In humans, the rhythmicity of sweet taste was evident in detection but not recognition thresholds, indicating circadian modulation at the level of primary sensory processing rather than higher-order cognitive processes. In rats, increased sensitivity during the dark phase was accompanied by upregulation of taste-related genes in type II taste cells in tongue. These findings provide evidences that circadian regulation of taste sensitivity is conserved across species and appears to operate predominantly at the peripheral level. This mechanism may have evolved to optimize energy intake while minimizing exposure to dietary toxins, potentially contributing to survival and continuing to influence modern eating behavior through circadian-sensory-nutritional interactions.

physiology↗

bioRxiv2026

Systemic injection of metabotropic glutamate 2/3 receptor antagonist LY341495 disrupts reward-related behaviors in mice.

Metabotropic glutamate 2/3 receptors (mGluR2/3) have been implicated in depression, anxiety, learning, and memory, yet their role in reward-related behavior remains poorly understood. Here, we examined the effects of the selective mGluR2/3 antagonist LY341495 on reward-related behaviors in mice using a combination of head-fixed and freely moving behavioral paradigms. In a head-fixed temporal conditioning task, mice developed anticipatory licking and pupil dilation preceding the delivery of a 10% sucrose solution, indicating successful temporal anticipation of reward. Systemic administration of LY341495 dose-dependently reduced both anticipatory and consummatory licking. Normalization analyses further suggested that LY341495 reduced the overall expression of licking behavior while largely preserving its temporal organization. LY341495 also induced pupil dilation and attenuated reward-proximity-related pupillary modulation. To determine whether these effects reflected non-specific motor impairments, we assessed locomotor activity in an open-field task and measured ultrasonic vocalizations (USVs) during courtship interaction. LY341495 did not significantly alter locomotion, excretion, or USV production, suggesting preserved general motor and orofacial motor function. In contrast, LY341495 dose-dependently reduced food intake and decreased social preference, indicating that the effects of mGluR2/3 antagonism extend beyond ingestive behavior to social reward-related processes. These findings demonstrate that mGluR2/3 signaling contributes to the regulation of reward-related behaviors across multiple reward domains independently of general motor dysfunction. These results provide new insight into glutamatergic mechanisms underlying motivation and reward processing and may have implications for neuropsychiatric disorders characterized by anhedonia and motivational deficits.

neuroscience↗

bioRxiv2026

geneSTRUCTURE: A Modern Platform for Visualization of Gene Structures

Even in the era of genomics and pan-genomics, the gene remains the fundamental unit of heredity. Accurate visualization of gene structures provides essential insights into the organization, regulation, and evolution of each gene. Representing elements such as exons, introns, untranslated regions, and functional domains in a clear and interpretable format is particularly important for analyzing complex gene architectures and for communicating results effectively. Despite the availability of several visualization tools, many are limited in their ability to incorporate user-defined annotations or to support interactive and customizable figure generation, which reduces their utility in modern analytical workflows. To address these limitations, we developed geneSTRUCTURE, both command-line-interface and web-based application designed to provide flexible and user-friendly visualization of gene structures based on widely used annotation formats, GFF3 and GTF. In addition to visualizing core gene components, the platform allows users to overlay supplemental annotations, including mutation sites and protein domains, and to adjust layout features in real time. By combining a modern interface with annotation flexibility and high-resolution output, geneSTRUCTURE offers a robust solution for gene-level visualization.

bioinformatics↗

bioRxiv2026

Fragile streak goals induce pressure responses and an inverted-U performance pattern

Psychological pressure is thought to relate to performance in an inverted-U pattern, yet evidence is mixed, possibly because manipulations rarely produce high pressure. We induced scalable pressure using a streak goal that resets after a failure in a force-control task. Participants pursued ten consecutive successes (streak goal) or 100 successes irrespective of sequence (total goal). Under the streak goal, heart rate, pupil size, and perceived pressure rose as participants approached their maximum streak; under the total goal, heart rate and pupil size showed little modulation. Performance followed an inverted-U under the streak goal--improving then declining at the maximum streak--whereas the total goal showed no late-stage drop. This dissociation suggests the late-stage decline reflects pressure, not the streak itself. Despite this clear performance decrement, analyses of movement vigor, feedforward/feedback kinematics, and individual differences in pressure responses revealed no consistent systematic signatures at the group level. Fragile streak goals thus provide a multimodal pressure manipulation and a platform for testing mechanisms underlying choking in human motor control.

neuroscience↗

bioRxiv2026

Organyl 5'-Phosphates in siRNA Guide Strands: Structure-Function Relationships Governing Anchoring in Argonaute 2 and Metabolic Stability

Efficient siRNA loading into Argonaute2 (AGO2) requires a 5'-phosphate (5'-P) on the guide strand, yet this group is vulnerable to metabolic degradation in vivo. Although numerous chemical mimics of 5'-P have been reported, structural principles governing AGO2 interactions with organyl substituents on the 5'-P remain unclear. Moreover, structural determinants of 5'-P mimic recognition by known degradative enzymes (principally phosphatases and 5'-exonucleases) are also poorly understood. The 5'-P binding site of the AGO2 MID domain contains a stack of aromatic residues (Y527/F811/Y815), presenting a structural basis for augmenting canonical anchoring interactions. Herein, we systematically synthesized and characterized a diverse panel of organyl 5'-phosphates (5'-POR; R = 35 variable substituents) as guide strand 5'-P mimics designed to engage this unique hydrophobic pocket. Among the compounds evaluated, 5'-POR guide strands bearing methyl (Me) or phenylpropargyl (PhPrp) substituents are well-tolerated by AGO2 in cells. Previously uncharacterized 5'-P mimics, including 5'-phosphorothioate (5'-PS), phenylpropargyl 5'-phosphorothioate (5'-PS-PhPrp), and 5'-mesylphosphoramidate (5'-MsPA), maintain comparable AGO2 compatibility. All examined 5'-P mimics are markedly resistant to phosphatase, while 5'-POR variants and 5'-PS-PhPrp are also resistant to 5'-exonuclease degradation due to masking a negative charge of 5'-P. A crystal structure of a 5'-PO-PhPrp guide strand loaded into AGO2 reveals an unexpected network of {pi}-{pi} interactions between the rigid phenylpropargyl group and the targeted hydrophobic pocket of the MID domain. Collectively, these findings expand the functional chemical space of 5'-P mimics and define new modes for metabolically stabilizing the guide strand 5'-end while augmenting AGO2 MID anchoring. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/705631v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@e6f88forg.highwire.dtl.DTLVardef@1c87dfaorg.highwire.dtl.DTLVardef@1c6e68corg.highwire.dtl.DTLVardef@14a1f60_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

L-Phenylalanine restriction amplifies boron neutron capture therapy efficacy through increased L-boronophenylalanine uptake and induces activating transcription factor 4 stress response in tumor cell lines

Boron neutron capture therapy (BNCT) relies on the selective uptake of boron-10 compounds by tumor cells. L-boronophenylalanine (BPA) serves as a key carrier, and enhancing its accumulation is critical for improving BNCT efficacy. In this study, we investigated the effects of L-phenylalanine (Phe) restriction on the tumor cell lines SAS, U87-MG, PANC-1, and A375, and the immortalized keratinocyte line HaCaT on modulating BPA uptake and associated cellular responses. Quantitative analysis using inductively coupled plasma atomic emission spectroscopy (ICP-AES) showed that 24 h Phe restriction increased BPA uptake in the SAS, U87-MG, and PANC-1 cell lines. Colony formation assays confirmed enhanced sensitivity to neutron irradiation in these cells. RNA sequencing indicated that Phe restriction activated the integrated stress response downstream of activating transcription factor 4 (ATF4), although this pathway was not directly linked to increased BPA uptake. The L-type amino acid transporter 1 (LAT1)/4F2 heavy chain (4F2HC) complex was identified as the exclusive transport route for BPA. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis showed that Phe restriction altered intracellular levels of amino acids that serve as LAT1/4F2HC exchange substrates, suggesting a metabolic basis for enhanced BPA transport. Our results reveal that Phe restriction enhances BPA uptake and BNCT efficacy in a cell line-dependent manner, likely through the modulation of amino-acid metabolism. Therefore, targeted amino-acid manipulation prior to BNCT may represent a promising strategy to improve therapeutic outcomes.

cancer biology↗

bioRxiv2025

PhenoDEL as a Novel Screening Strategy Based on Intracellular Protein Degradation Activity

Targeted protein degradation (TPD), including proteolysis targeting chimeras (PROTACs) and molecular glue degraders (MGDs), is a promising therapeutic approach. However, systematic discovery of such small molecules remains a major challenge. Here, we present PhenoDEL, a novel phenotypic DNA-encoded library (DEL) screening platform that integrates one-bead one-compound DEL (OBOC-DEL) with the Beacon(R) optofluidic system for high-throughput, single-cell analysis. By co-culturing individual OBOC-DEL beads and engineered reporter cells in nanoliter-scale chambers, PhenoDEL enables direct observation of compound-induced protein degradation at single-cell resolution. We demonstrate this approach by identifying compounds that induce degradation of FKBP12F36V-EGFP fusion proteins in PC-3 cells. The workflow allows precise linkage between compound identity and cellular phenotype via DNA barcoding and next-generation sequencing. PhenoDEL overcomes limitations of conventional screening methods, offering high sensitivity, spatial control, and scalability. This platform holds significant potential for mechanism-driven drug discovery, including identification of novel PROTACs and MGDs. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/690606v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@fe27bforg.highwire.dtl.DTLVardef@1e38ef5org.highwire.dtl.DTLVardef@be958aorg.highwire.dtl.DTLVardef@4bc48a_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

The Paradox of Unpredictability: Trying to Be Unpredictable Makes Sequences More Predictable

Human intuition about randomness is systematically biased. When asked to generate random sequences, people systematically generate too many alternations, yet game theory suggests that being unpredictable to an opponent requires true randomness. In our first experiment (50 Japanese adults), we show that when the goal shifts from being random to being unpredictable, participants do the opposite, generating sequences with a strong repetition bias. In a second experiment, we asked a new sample of 50 Japanese adults to predict two model-derived sequences that were empirically calibrated to the group-level statistics from the first Experiment (Competitive-like vs Random-like). We found a paradox: the repetitive sequences intended to be unpredictable were in fact more predictable than the alternating sequences intended to be random. This paradox appears to stem from an asymmetric reinforcement learning mechanism, whereby success selectively strengthens beliefs in repetition but not alternation. Our findings bridge classic cognitive bias and strategic behavior, suggesting how a fundamental learning mechanism can shape paradoxical predictability.

neuroscience↗

bioRxiv2025

Structure-guided development of a potent human B0AT1 inhibitor effective in a mouse model of phenylketonuria

B0AT1 is a neutral amino acid transporter responsible for the (re)absorption in the intestine and kidney. Here, we developed small-molecule inhibitors of B0AT1 as a therapeutic strategy to a transient pocket, located [~]17 [A] away from the substrate-binding site and unique to the outward-open conformation, and stabilize an outward-occluded conformation that prevents the conformational transitions required for transport. Guided by structural insights, we optimized an initial inhibitor (Cinromide) to improve potency and cross-species activity, yielding compound 3, which inhibits both human and mouse B0AT1 with submicromolar IC_50 values. In a PKU mouse model (Pahenu2), oral administration of compound 3 increased urinary Phe excretion and significantly reduced plasma Phe. Our findings identify a druggable allosteric site in B0AT1, demonstrate its utility for achieving potent and selective inhibition in vivo, and establish allosteric blockade as a therapeutic approach for PKU and other SLC6-family transporters.

pharmacology and toxicology↗

bioRxiv2025

Sex-biased transcriptome in embryonic mouse cortices under Pax6 haploinsufficiency highlights Pbdc1 as a candidate regulator

Mutations in Pax6, encoding a transcription factor essential for brain patterning and neurogenesis, have been linked to female-biased cortical malformations and behavioral abnormalities, yet the molecular basis remains unclear. Here we show that Pax6 haploinsufficiency (Sey/+) produces more pronounced sex-biased alterations in the transcriptomes and cytoarchitecture of embryonic mouse cortices than those in wild-type and homozygous mutants (Sey/Sey). Pbdc1, a previously uncharacterized X-linked gene implicated in autism, is selectively upregulated in Sey/+ females and proximity-dependent protein-protein interaction analysis reveals Pbdc1 interacts with RNA-splicing factors. Moreover, Pbdc1 overexpression reduces intermediate progenitor cells in the developing cortex. ChIP-qPCR further demonstrates Pax6 and BAF occupancy at the Pbdc1 promoter in WT embryos of both sexes and CUT&Tag shows H3K4me3 elevation selectively in Sey/+ females. Our findings indicate that partial loss of Pax6 shapes the embryonic cortical transcriptomes and cytoarchitecture in a sex-dependent manner and highlight Pbdc1 as a candidate regulator of sex-biased corticogenesis.

developmental biology↗

bioRxiv2025

Autoclaving and long-term storage deplete glutamine sources in complex media and affect bacterial phenotypes

Autoclave sterilization is the most common method for sterilizing reagents and media in biology. However, the effects of heat-induced loss or modification of complex medium components on bacterial growth and phenotypes remain poorly understood. Here, we investigated the impact of autoclaving on glutamine sources in bacterial complex media using an Escherichia coli {Delta}glnA mutant, which requires exogenous glutamine for growth. {Delta}glnA exhibited impaired growth in LB medium after autoclaving compared with non-autoclaved LB, whereas its residual growth indicated the presence of heat-stable glutamine sources. Growth assays and HPLC quantification revealed that free glutamine in LB decreased from 58 {micro}M to 12 {micro}M upon autoclaving, while heat-stable glutamine sources remained at 117 {micro}M. Similar growth defects were observed for {Delta}glnA in autoclaved BHI, TSB, and M17 media compared with their non-autoclaved counterparts. Long-term storage of LB at room temperature for 24 weeks also reduced {Delta}glnA growth regardless of autoclaving, compared with freshly prepared LB. Furthermore, supplementation of glutamine sources into glutamine-deficient MHB medium enhanced biofilm formation by Pseudomonas aeruginosa. Collectively, these results demonstrate that autoclaving and storage reduce glutamine sources in complex media, thereby influencing bacterial growth and phenotypes.

microbiology↗