Biology subjects

Wang, M.

Publications and source records attributed to Wang, M..

At least 235 records · Page 13Linked to original sources

bioRxiv2025

3'UTR-derived small RNA couples acid resistance to metabolic reprogramming of Salmonella within macrophages

Acid resistance is crucial for enterobacteria to withstand host acidic environments during infection, including the gastrointestinal tract and macrophage phagosomes. A key acid resistance mechanism of the facultative intracellular pathogen Salmonella is expression of the arginine decarboxylase AdiA. While AdiA confers acid resistance via an H+-consuming reaction, we discover that the 3'-untranslated region (UTR) of adiA mRNA is processed by RNase E into a regulatory small RNA, AdiZ. Through RNA-RNA interactome profiling and transcriptomic analysis, followed by in vitro structural probing and in vivo validations, we demonstrate that AdiZ directly base-pairs with and negatively regulates ptsG, pykF, and dmsA mRNAs involved in glucose uptake, glycolysis, and anaerobic respiration, respectively. Intriguingly, AdiZ is induced and facilitates Salmonella survival within macrophages, where acidic and hypoxic stresses prevail. Thus, simultaneous expression of AdiA and AdiZ from a single mRNA ties arginine-dependent acid resistance to metabolic reprogramming of Salmonella in the host intracellular niches. HIGHLIGHTSO_LISalmonella adiA transcript expresses both acid resistance enzyme and sRNA AdiZ C_LIO_LIAdiZ derived from the adiA 3'UTR is induced under an acidic and anaerobic condition C_LIO_LIAdiZ base-pairs with mRNAs to modulate glucose metabolism and anaerobic respiration C_LIO_LIAdiZ promotes Salmonella survival in acidic and hypoxic macrophage vacuoles C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/658255v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@10aec22org.highwire.dtl.DTLVardef@14b5f2org.highwire.dtl.DTLVardef@1b53c8dorg.highwire.dtl.DTLVardef@19a8540_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Senescent mast cells contribute to the progression of benign prostatic hyperplasia via SCF/c-KIT mediated endothelial-mesenchymal transition

Benign prostatic hyperplasia (BPH) is a common age-associated urological condition characterized by stromal expansion, but its cellular origins and regulatory mechanisms remain unclear. In this study, we identified endothelial-to-mesenchymal transition (EndMT) as a contributor to stromal cell accumulation in BPH. Using single-cell transcriptomic analysis, endothelial lineage tracing in mice, and validation in human samples, we showed that senescence-associated mast cells increased the expression of vascular endothelial growth factor A (VEGFA) and transforming growth factor-beta 1 (TGF-{beta}1) through the stem cell factor (SCF)/c-KIT-MAPK-JUND signaling pathway, thereby inducing EndMT in endothelial progenitor cells. Stromal fibroblasts express SCF, promoting mast cell activation and establishing a feedback loop that supports continued stromal proliferation. Intriguingly, inhibition of mast cell activation reduces EndMT and attenuates prostate enlargement in vivo. Thus, these findings revealed a senescence-linked immune-stromal interaction in the aging prostate and identify potential targets for therapeutic intervention in BPH.

cell biology↗

bioRxiv2025

Genome-Bench: A Scientific Reasoning Benchmark from Real-World Expert Discussions

In this short report, we present an automated pipeline tailored for the genomics domain and introduce Genome-Bench, a new benchmark constructed from over a decade of scientific forum discussions on genome engineering. Our pipeline transforms raw interactions into a reinforcement learningfriendly multiple-choice questions format, supported by 3000+ high-quality questionanswer pairs spanning foundational biology, experimental troubleshooting, tool usage, and beyond. To our knowledge, this is the first end-to-end pipeline for teaching LLMs to reason from scientific discussions, with promising potential for generalization across scientific domains beyond biology. The dataset is available at https://huggingface.co/datasets/Mingyin0312/Genome-Bench.

genomics↗

bioRxiv2025

Autism-associated SCN2A deficiency disrupts cortico-striatal circuitry in human brain assembloids

Profound autism spectrum disorder (ASD) is frequently attributable to single-gene mutations, with SCN2A (voltage-gated sodium channel NaV1.2) protein-truncating variants (PTVs) being one of the most penetrant. Although cortico-striatal circuitry is implicated as a key node in ASD, the impact of SCN2A deficiency on human neural circuits is unknown. Using the human cortico-striatal assembloid model, we show that the autism-causing PTV SCN2A-C959X impairs long-range cortical axonal projections, reduces striatal spine density, and attenuates excitatory cortical-striatal synaptic transmission. Surprisingly, these assembloids carrying the heterozygous SCN2A nonsense mutation exhibited pronounced network hyperexcitability, a human cell-specific phenotype not observed in Scn2a+/- mice, highlighting a human-specific circuit vulnerability. Collectively, our study unveils human circuit-specific dysfunctions of SCN2A deficiency and SCN2A-mediated ASD. HighlightsO_LIAxonal projections facilitate synapse formation and functional connectivity in human brain assembloids. C_LIO_LINaV1.2 is expressed along neuronal axons, extending to soma and dendrites in human brain assembloids. C_LIO_LISCN2A-C959X disrupts axonal projection patterns, impairs excitatory synaptic transmission, reduces spine density, and results in elevated neuronal excitability. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/657036v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@6d5b1forg.highwire.dtl.DTLVardef@1795ecdorg.highwire.dtl.DTLVardef@13f0d7eorg.highwire.dtl.DTLVardef@8ee059_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefO_ST_ABSSCN2A haploinsufficiency impairs cortico-striatal circuitry.C_ST_ABSSCN2A haploinsufficiency disrupts axon initial segment (AIS) integrity, leading to hyperexcitability (red arrow), reduced axon projections, and impaired synaptic transmission (decreased sEPSCs and altered network firing). These deficits result in dysfunction within the cortico-striatal circuitry.

neuroscience↗

bioRxiv2025

Biomni: A General-Purpose Biomedical AI Agent

Biomedical research underpins progress in our understanding of human health and disease, drug discovery, and clinical care. However, with the growth of complex lab experiments, large datasets, many analytical tools, and expansive literature, biomedical research is increasingly constrained by repetitive and fragmented workflows that slow discovery and limit innovation, underscoring the need for a fundamentally new way to scale scientific expertise. Here, we introduce Biomni, a general-purpose biomedical AI agent designed to autonomously execute a wide spectrum of research tasks across diverse biomedical subfields. To systematically map the biomedical action space, Biomni first employs an action discovery agent to create the first unified agentic environment - mining essential tools, databases, and protocols from tens of thousands of publications across 25 biomedical domains. Built on this foundation, Biomni features a generalist agentic architecture that integrates large language model (LLM) reasoning with retrieval-augmented planning and code-based execution, enabling it to dynamically compose and carry out complex biomedical workflows - entirely without relying on predefined templates or rigid task flows. Systematic benchmarking demonstrates that Biomni achieves strong generalization across heterogeneous biomedical tasks - including causal gene prioritization, drug repurposing, rare disease diagnosis, micro-biome analysis, and molecular cloning - without any task-specific prompt tuning. Real-world case studies further showcase Biomnis ability to interpret complex, multi-modal biomedical datasets and autonomously generate experimentally testable protocols. Biomni envisions a future where virtual AI biologists operate alongside and augment human scientists to dramatically enhance research productivity, clinical insight, and healthcare. Biomni is ready to use at https://biomni.stanford.edu, and we invite scientists to explore its capabilities, stress-test its limits, and co-create the next era of biomedical discoveries.

bioinformatics↗

bioRxiv2025

Neural Spectral Prediction for Structure Elucidation with Tandem Mass Spectrometry

Structural elucidation using untargeted tandem mass spectrometry (MS/MS) has played a critical role in advancing scientific discovery [1, 2]. However, differentiating molecular fragmentation patterns between isobaric structures remains a prominent challenge in metabolomics [3-10], drug discovery [11-13], and reaction screening [14-17], presenting a significant barrier to the cost-effective and rapid identification of unknown molecular structures. Here, we present a geometric deep learning model, ICEBERG, that simulates high-energy collision-induced dissociation in mass spectrometry to generate chemically plausible fragments and their relative intensities with awareness of collision energies and polarities. We utilize ICEBERG predictions to facilitate structure elucidation by ranking a set of candidate structures based on the similarity between their predicted in silico MS/MS spectra and an experimental MS/MS spectrum of interest. This integrated elucidation pipeline enables state-of-the-art performance in compound annotation, with 40% top-1 accuracy on the NIST20 [M+H]+ adduct subset and with 92% of correct structures appearing in the top ten predictions in the same dataset. It achieves 46% top-1 and 86% top-10 accuracies when tested on the open-access MassSpecGym benchmark, and outperforms SIRIUS on a recently released test set with previously uncharacterized structures. We demonstrate several real-world case studies, including identifying clinical biomarkers of depression and tuberculous meningitis, annotating an aqueous abiotic degradation product of the pesticide thiophanate methyl, disambiguating isobaric products in pooled reaction screening, and annotating biosynthetic pathways in Withania somnifera. Overall, this deep learning-based paradigm for structural elucidation enables rapid molecular annotation from complex mixtures, driving discoveries across diverse scientific domains.

bioinformatics↗

bioRxiv2025

Structural innovations and neurogenic continuity define avian brain development and evolution

Understanding how neurogenic diversity and brain architecture emerge is crucial for deciphering the mechanisms of brain plasticity and cognitive evolution. Here, we present a comprehensive single-cell and spatial transcriptomic atlas of the budgerigar brain, a highly cognitive avian species. We uncover a striking dorsoventral symmetry in excitatory neuron distribution, precisely organized along the lamina mesopallialis intermedia (LMI), a key boundary structure. Cross-species comparisons further reveal the origins of this unique avian pallial organization, offering new insight into avian brain evolution. Our study also highlights distinct developmental trajectories and asynchronous maturation patterns between telencephalic and optic tectum excitatory neurons, underscoring their contribution to innate circuit assembly. Furthermore, we identify adult neural stem cells (NSCs) with evolutionarily conserved transcriptomic signatures across avian species, emphasizing their role in brain plasticity and adaptation. These findings refine fundamental models of avian brain development and elucidate conserved principles of cognitive plasticity.

evolutionary biology↗

bioRxiv2025

TIP-seq: A Single-cell Multiomics Approach for Simultaneous Transcriptome and Intracellular Protein Profiling

Single-cell multiomics technologies have significantly advanced our understanding of cellular heterogeneity; however, the concurrent profiling of mRNA transcripts and target proteins continues to pose a substantial challenge. To bridge the gap between single-cell sequencing and proteomic methods, we developed an innovative single-cell multiomics methodology, termed TIP-seq, which facilitates the simultaneous profiling of the transcriptome and intracellular proteins without prior cell manipulation. In TIP-seq, microfluidic technology is leveraged to integrate oligonucleotide-labeled antibodies with hydrogel beads, allowing for the capture of mRNAs and proteins from individual cells within droplets, thereby enabling high-throughput and precise dual-omics data acquisition. When applied to lung cell lines and non-small cell lung cancer (NSCLC) tissues, TIP-seq analysis revealed notable cellular heterogeneity and molecular dynamics, emphasizing the distinct immune cell interactions within NSCLC tissues. Key immune checkpoint interactions in NSCLC, such as SPP1-CD44, NECTIN2-TIGIT, and NECTIN2-CTLA4, along with functional alterations in tumor-associated dendritic cells (DCs) and T cells, were identified via TIP-seq, underscoring their pivotal roles in mediating immune suppression within the tumor microenvironment. Collectively, TIP-seq represents a powerful methodology for identifying novel therapeutic targets and biomarkers, thereby holding significant potential for the advancement of precision medicine in the treatment of lung cancer and other complex diseases.

biochemistry↗

bioRxiv2025

Box C/D snoRNPs and MDT-15/MED15 regulate mitochondrial surveillance via fatty acid metabolism

Text AbstractIn response to constant homeostatic threats, organisms have developed complex regulatory networks to monitor cellular functions and restore normal function. Here, we identify MDT-15 and its effectors, the fatty acid desaturases FAT-5, FAT-6, and FAT-7, as activators of the Ethanol and Stress Response (ESRE) mitochondrial surveillance pathway. Our data show that box C/D snoRNPs, which were previously linked to ESRE activation, also regulate FAT-6 and FAT-7 protein levels. Notably, knockdown of mdt-15 or fib-1, a component of box C/D snoRNP complex, increased accumulation of the mitophagic activator PINK-1, the first step in licensing mitophagy, suggesting a relationship between ESRE surveillance and mitophagic activation. Supplementation with downstream unsaturated fatty acid products of FAT-6 and FAT-7 enhanced ESRE and mitophagic activation, but did not affect UPRmt. Since fatty acids activated ESRE and PINK-1 in wild-type and mutant genetic backgrounds, they are likely to act via a mechanism independent of FAT-6 and FAT-7 function. Our results provide insight into a novel interplay between box C/D snoRNPs, MDT-15, and fatty acids in the regulation of mitochondrial surveillance and mitophagy. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/656193v2_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@92f749org.highwire.dtl.DTLVardef@a8f496org.highwire.dtl.DTLVardef@51b28dorg.highwire.dtl.DTLVardef@1a15374_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Metabolic basis of the astrocyte-synapse interaction governs dopaminergic-motor connection

Perisynaptic astrocyte processes are constitutive attachments of synapses in the central nervous system. However, the molecular mechanisms that control perisynaptic astrocyte ensheathment and their implications in the wiring of neural circuits remain unclear. Here, we report that glycolysis controls astrocyte-synapse contact. In the Drosophila larval dopaminergic (DAergic) circuit, blocking astrocyte glycolysis stimulated perisynaptic ensheathment by attenuating astrocyte-to-DAergic neuron neuroligin 2-neurexin 1 signaling. As a result, the larvae executed more reorientation actions during locomotion. At the circuit level, behavioral alterations were found to arise from increased DAergic neuronal synaptogenesis and DAergic-motor connection. Our research uncovers an ancient metabolic basis that determines perisynaptic astrocyte ensheathment abundance through a conserved neuroligin-neurexin signaling pathway and demonstrates the role of astrocyte glycolysis in controlling DAergic-motor circuit assembly and function.

neuroscience↗

bioRxiv2025

Neuronal feedback loop in the suprachiasmatic nucleus generates robust circadian rhythms

The central circadian clock of the suprachiasmatic nucleus (SCN) is a network consisting of various types of neurons and glial cells, but its mechanism remains elusive. Here, by monitoring cellular calcium rhythms in vivo in vasoactive intestinal polypeptide (VIP)-deficient mice, we show that arginine vasopressin (AVP) neurons intrinsically oscillate with a short period and that VIP amplifies and delays the AVP neuronal rhythm to lengthen its period to [~]24 hours. Consistently, the circadian behavior period is shortened and lengthened by VIP receptor disruption and neurotransmission blockade of AVP neurons, respectively. VIP and other neurons occasionally exhibit weak, unstable, long-period calcium rhythms only when AVP neuronal oscillation is attenuated. Together with our previous finding that AVP neurons act as the primary pacesetter cells of the SCN ensemble rhythm, our results indicate that the feedback neuronal circuit of AVP cellular oscillator and VIP peptide signaling is crucial for the robust circadian rhythm.

neuroscience↗

bioRxiv2025

Fusion transcription factor dosage controls cell state in rhabdomyosarcoma

In the fusion-positive subset of rhabdomyosarcoma, the PAX3::FOXO1 oncoprotein is the most common fusion driver. We previously established a human myoblast system for inducible expression of PAX3::FOXO1. In the current study, we modulate PAX3::FOXO1 protein expression to understand the epigenetic and phenotypic functions at different PAX3::FOXO1 levels. Proliferative and oncogenic outcomes depend on PAX3::FOXO1 dosage in this system with transformation dominant at intermediate levels and growth suppression dominant at high levels. After prolonged PAX3::FOXO1 expression, there is dosage-dependent heterogeneity in single cell gene expression profiles. We observe a dosage-specific effect for PAX3::FOXO1 chromatin recognition and identify factors that modulate PAX3::FOXO1 chromatin binding. PAX3::FOXO1 dosage affects expression signatures related to cell cycle, epithelial-mesenchymal transition, and myogenesis. Whereas intermediate PAX3::FOXO1 expression maximizes chromatin binding to modulate gene expression, high PAX3::FOXO1 expression alters S phase progression and increases accessibility behind the replication fork. We conclude that PAX3::FOXO1 exerts dosage-dependent functions to influence epigenetic heterogeneity in fusion-positive rhabdomyosarcoma.

genomics↗

bioRxiv2025

Retinal nerve fibre layer thickness reflects characteristics of brain grey and white matter

The retina is a relatively accessible part of the central nervous system compared to the brain. Using high resolution optical imaging we investigated the relationship between retinal thickness, obtained with optical coherence tomography, and structural features of the brain obtained with magnetic resonance imaging. In a population-based sample of over 500 subjects, we hypothesized: (i) that there are structural associations between circumpapillary retinal nerve fibre layer thickness and brain grey matter density and white matter microstructural properties in visual information processing areas, and specifically contralateral associations for nasal retinal fibers, and (ii) that retinal findings reflect broader changes in brain grey and white matter related to cardiovascular risk factors. In support of the first hypothesis, we showed associations of circumpapillary retinal nerve fibre layer thickness with visual cortex grey matter density and with optic radiation fractional anisotropy. These correlations were stronger for the right eye, possibly reflecting right ocular dominancy. Regarding the second hypothesis, while we confirmed the broad impact of cardiovascular risk factors such as body mass index, diabetes, and hypertension on brain structure, we didnt find (adequate) significant partial correlations between circumpapillary retinal nerve fibre layer thickness and cardiovascular risk factors to support the hypothesis. As such, we couldnt confirm that circumpapillary retinal nerve fibre layer thickness is associated with the impact of cardiovascular risk factors on the brain structure. However, when the effects of cardiovascular risk factors were accounted for statistically, circumpapillary retinal nerve fibre layer thickness (particularly on the right side) was associated with fractional anisotropy of limbic system tracts, i.e., the fornix and stria terminalis including hippocampus and amygdala. To further explore the structural associations between eye and brain, in terms of a possible common underlying pathology related to cardiovascular risk factors and progressive neurodegenerative diseases on the central nervous system, longitudinal and interventional studies are necessary.

neuroscience↗

bioRxiv2025

Transient centrosome loss in cultured prostate epithelial cells induces chromosomal instability to produce an oncogenic genotype that correlates with poor clinical outcomes

Chromosomal instability (CIN) is a hallmark of prostate cancer that strongly correlates with metastatic burden and appears prominently in both primary cancer and metastatic disease. Low Gleason score primary prostate tumors display pervasive centrosome loss, a known mechanistic driver of CIN, that disrupts normal spindle assembly and increases mitotic errors. Previously, we found that transient depletion of centrosomes in immortalized, non-tumorigenic prostate epithelial cells (PrEC) induced a burst of CIN, generating cell lines capable of forming xenograft tumors. Here, we use a multi-omics approach to identify the oncogenic alterations caused by transient centrosome loss. By integrating genomic and transcriptomic data of the prostate lines, we identified a consensus set of focal copy-number variations (CNVs) induced by centrosome loss in cultured cells that are also detectable within a subset of samples from a prostate cancer patient cohort. Using this CNV signature, we were able to derive a unique transcriptomic signature from prostate cancer patient samples that showed strong predictive value for adverse clinical outcomes. In summary, our experimental system uses centrosome loss to promote a punctuated burst of genomic crisis that is characteristic of genome evolution during prostate cancer progression. Consequently, this prostate cancer model produced recurrent structural variations that are detectable in patient samples and associate with worse outcomes. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/653266v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@ac4c9org.highwire.dtl.DTLVardef@fd9961org.highwire.dtl.DTLVardef@160e20corg.highwire.dtl.DTLVardef@198bf0e_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

A census of anti-CRISPR proteins reveals AcrIE9 as an inhibitor of Escherichia coli K12 Type IE CRISPR-Cas system

CRISPR-Cas adaptive immunity systems provide defense against mobile genetic elements and are often countered by diverse anti-CRISPR (Acr) proteins. The Type IE CRISPR-Cas of Escherichia coli K12 has been a model for structural and functional studies and is a part of the species core genome. However, this system is transcriptionally silent, which has fueled questions about its true biological function. To clarify the role of this system in defense, we carried out a census of Acr proteins found in Enterobacterales and identified AcrIE9 as a potent inhibitor of the E. coli K12 Type IE CRISPR-Cas system. While sharing little sequence identity, AcrIE9 proteins from Pseudomonas and Escherichia both interact with the Cas7 subunit of the Cascade complex, thus preventing its binding to DNA. We further show that AcrIE9 is genetically linked to AcrIE10, forming the most widespread anti-CRISPR cluster in Enterobacterales, and this module often co-occurs with a novel HTH-like protein with unusual architecture.

microbiology↗

bioRxiv2025

IRE1α and IRE1β Protect Intestinal Epithelium and Suppress Colorectal Tumorigenesis through Distinct Mechanisms

Intestinal epithelial cells (IECs) uniquely express two IRE1 paralogues, IRE1 and IRE1{beta}, whose roles in intestinal physiology are incompletely understood. We examined the individual and cooperative functions of IRE1 and IRE1{beta} in IECs using mice using intestine-specific deletion of Ire1 or germline Ire1{beta} deletion, and subsequently with double deleted Ire1, Ire1{beta} mice. At baseline, intestine-specific Ire1 deleted mice and mice with germline Ire1{beta} deletion exhibited no morphologic changes in small intestine or colon, but double deleted Ire1-/-Ire1{beta}-/- mice developed progressive intestinal and colonic injury and tumorigenesis. In contrast to single-deleted IECs, RNA-Seq from Ire1-/-Ire1{beta}-/- IECs revealed decreased expression of defense-associated mRNAs, together with increased expression of inflammatory and pathogenic mRNAs. Utilizing orthogonal models of intestinal tumorigenesis, reflecting either inflammatory-mutagenic injury (AOM-DSS) or spontaneous polyposis (APCmin), we observed that loss of either intestinal epithelial Ire1 or of Ire1{beta} alone produced a growth advantage, increasing tumor burden. IRE1 mediated splicing of Xbp1 mRNA was maintained following Ire1{beta} deletion but not in double deleted Ire1-/-Ire1{beta}-/- mice. Increased expression of either Ire1 or Ire1{beta} mRNA was associated with improved survival in patients with colorectal cancer. Taken together our findings suggest IRE1 paralogues utilize essential but distinct mechanisms to safeguard intestinal homeostasis and suppress tumorigenesis.

cancer biology↗

bioRxiv2025

Substitutions in RNA-binding protein Hrp1 map a potential interaction surface with the yeast RNA polymerase II elongation complex

Anti-termination factors for eukaryotic RNA polymerase II (RNAP II) that are released upon binding sequences in the terminator of nascent transcripts were proposed almost 40 years ago but few candidates have been found. Here we report genetic evidence that the yeast nuclear RNA-binding protein Hrp1, also known as Nab4 and CF1B, acts as an RNAP II anti-termination factor. A Lys to Glu substitution at residue 9 (K9E) of the Rpb3 subunit of RNAP II causes readthrough of Nrd1-Nab3-Sen1-dependent (NNS) terminators and cold-sensitive growth, as does Asp but not Ala, Met, Arg, or Gln substitution. These allele-specific phenotypes and the location of Rpb3-K9 suggests substitution with Glu or Asp stabilizes binding of an anti-termination factor via a salt bridge. A genome-wide selection for suppressors of the cold-sensitivity of Rpb3-K9E yielded an Arg to Gly substitution at residue 317 of Hrp1 in RNA recognition motif 2 (RRM2), consistent with the hypothesis. A targeted selection for suppressors of Rpb3-K9E in HRP1 yielded substitutions in RRMs 1 and 2, an essential Met- and Gln-rich region C-terminal to the RRMs, and other mutations. We propose that Hrp1 binds to the RNAP II elongation complex via these regions to promote elongation and, in the presence of Rpb3-K9E, is less rapidly released upon binding terminator sequences in the nascent transcript, resulting in terminator readthrough. The Rpb3-K9E-suppressor substitutions in Hrp1 likely weaken binding to the RNAP II elongation complex, compensating for Rpb3-K9E.

molecular biology↗

bioRxiv2025

PIBE: Parallel ion beam etching of sections collected on wafer for ultra large-scale connectomics

We developed a parallel ion beam etching device that simultaneously thins hundreds of sections on a whole 4-inch wafer at 20 nm steps, enabling sub-centimeter volumetric imaging with high axial resolution. Compared with traditional volume electron microscopy, PIB preserves in-situ continuity within sections and simplifies inter-section registration. Its high axial resolution facilitates reliable neuron segmentation and tracing with reduced proofreading, providing an efficient route toward ultra-large-scale connectomics, such as whole-mouse-brain reconstruction.

neuroscience↗