Biology subjects

Wu, T.

Publications and source records attributed to Wu, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Follistatin-like 1 Promotes Neutrophil-mediated Host Defense against Klebsiella pneumoniae

Klebsiella pneumoniae is a leading cause of pneumonia and highly burdensome etiology of antibiotic-resistant infections constituting an urgent public health threat. Follistatin-like 1 (FSTL-1) is implicated in many processes including lung development and homeostasis, tissue remodeling, and inflammation though its role in antibacterial immunity remains poorly defined. We have observed that FSTL-1 is elevated in the lungs of both humans and mice during bacterial pneumonia. Using an inducible Fstl1 knockout mouse model, we demonstrate that FSTL-1 is required for pulmonary bacterial clearance and neutrophil recruitment during K. pneumoniae infection. Recombinant FSTL-1 rescues Fstl1-deficient susceptibility and enhances clearance of K. pneumoniae in wild-type mice. Mechanistically, FSTL-1-mediated protection was lost upon neutrophil depletion and in Cd14-deficient or Nr4a1 deficient mice, components of a lung-specific neutrophil transcriptional program. These findings identify FSTL-1 as a lung-derived factor that licenses neutrophil-mediated antibacterial defense via a novel FSTL-1/CD14/NR4A1-dependent signaling pathway critical for protection against bacterial pneumonia.

immunology↗

bioRxiv2026

NeCS-Flow: Necrosis-Guided Contrast-Enhanced MRI Synthesis with Rectified-Flow Refinement

Background: Gadolinium-based contrast agents raise concerns about tissue deposition, adverse reactions, and increased costs. Purpose: To develop and validate a deep learning pipeline for gadolinium-free post-contrast T1w brain MRI synthesis incorporating necrotic scaling and Posterior-Mean Rectified Flow (PMRF) refinement, and to evaluate diagnostic utility through a blinded multi-reader study. Study Type: Retrospective. Population: 454 patients with adult-type gliomas (grade 2-4) from four publicly available datasets. Training used 374 patients; internal testing used 60 held-out patients; external validation used 20 patients. Field Strength/Sequence: 1.5-3.0 T; pre-contrast T1w, T2w, and FLAIR as inputs; post-contrast T1w as synthesis target. Assessment: A three-stage pipeline comprising nnU-Net Necrotic core segmentation, necrotic-scaling-guided U-Net Contrast Synthesis, and PMRF perceptual refinement (NeCS-Flow) was evaluated using whole-brain and tumor-region similarity metrics, enhancing tumor Dice scores, perceptual quality metrics, and a blinded three-reader study assessing diagnostic accuracy, enhancement detection, image quality, and real-versus-synthetic discriminability. Statistical Tests: Paired t-tests and two one-sided tests for model comparison; Fisher's exact test and two-sample t-tests for reader study comparisons, with p < 0.05 considered significant. Results: Necrotic scaling consistently improved real versus synthetic enhancing tumor Dice internally (HGG: 0.793 to 0.816) and externally (HGG: 0.465 to 0.612). NeCS-Flow outperformed two benchmark architectures on all quantitative metrics in internal and external testing, although absolute enhancing tumor accuracy declined for all models on the external cohort. PMRF refinement improved perceptual realism across both tumor types, reducing both FID and KID. Readers distinguished synthetic from real images only modestly above chance (overall accuracy 61.7%), and no significant differences between real and synthetic images were found for any clinical metric. Data Conclusion: NeCS-Flow synthesizes perceptually realistic and diagnostically equivalent post-contrast T1w brain MRI, with necrotic scaling improving enhancing tumor delineation and PMRF refinement improving perceptual realism across gliomas. Performance on an external cohort was preserved relative to benchmark methods, though reduced in absolute terms.

bioinformatics↗

bioRxiv2026

Pseudomonas aeruginosa R-bodies deliver an ADP deaminase toxin

Diverse bacteria produce proteinaceous polymeric coils called R-bodies (refractile bodies), which extend into ~10 m-long needles in response to environmental triggers. It has been proposed that R-bodies deliver toxins intracellularly after such bacteria are ingested by eukaryotes, but intra-host extension of R-bodies has not been directly observed and these toxins remain unidentified. We use Pseudomonas aeruginosa PA14 and Dictyostelium discoideum to show that R-bodies extend within amoebae. We also identify a novel toxin, DeaR (deaminase associated with the R-body), which contributes to predation resistance and forms a near-megadalton dodecamer with ADP deaminase activity that alters purine metabolism. Our findings elucidate the molecular basis of R-body-mediated toxicity during PA14 infection and provide a paradigm for understanding the potential of cytotoxic effectors delivered by R-bodies (CEDRs) in interkingdom interactions.

microbiology↗

bioRxiv2026

Grow2Fold: mapping heterogeneous developmental growth to human brain folding

Cortical folding emerges through complex developmental processes, yet what organizes these processes into the characteristic folding patterns of the human brain remains unclear. Here, we developed an imaging-informed whole-brain modeling framework, Grow2Fold, that integrates developmental cortical regionalization, quantitative growth characterization, and mechanics-guided simulation to investigate how cortical growth shapes brain folding patterns. Using 836 fetal and neonatal MRI sessions from 747 participants spanning 21-45 postmenstrual weeks, we identified a reproducible and hierarchical spatiotemporal organization of cortical expansion characterized by coordinated regional growth trajectories. Rapid expansion occurs earlier around peri-central territories and progressively shifts toward frontal, parietal, and temporal association cortices. We encoded these imaging-derived trajectories into region- and age-specific growth laws and incorporated them into anatomically realistic whole-brain mechanical models. The resulting simulations recapitulate major sulcal landmarks and characteristic folding development across global and regional morphological measures. Comparing regional and uniform growth, we find that differential growth drives cortical instability, while heterogeneous developmental growth organizes this instability into anatomically recognizable folding patterns. Combined with subject-specific anatomy, these population-informed growth laws reproduce individualized longitudinal folding trajectories. Together, our results identify spatiotemporally patterned developmental growth as a key spatial constraint on cortical morphogenesis and establish a quantitative bridge from developmental imaging, through mechanical instability, to anatomically organized folding.

biophysics↗

bioRxiv2026

Autonomic and neurotrophic signaling in alcohol-associated liver disease

Alcohol-associated liver disease (ALD) is a leading cause of liver-related morbidity and mortality, yet its pathogenesis remains incompletely understood. While neural regulation is critical for hepatic homeostasis, how autonomic and neurotrophic signaling is regulated in the liver during ALD progression remains largely unexplored. Here, we performed an integrative analysis of bulk and single-cell transcriptomic datasets of human livers across the spectrum of ALD. We identified stage-dependent remodeling and coordinated expression patterns of autonomic and neurotrophic genes. Autonomic signaling exhibited a consistent decline, with reduced expression of sympathetic (DBH, TH) and the parasympathetic (ChAT) markers. In contrast, pan-neuronal and neuroplasticity-associated genes (UCHL1, TUBB3, STMN2) were upregulated, indicating active neural remodeling. In parallel, factors such as MANF, GDNF, and NRG2, with the receptor NTRK1, were upregulated and positively correlated with clinical indicators of disease severity, inflammation and fibrosis. In contrast, trophic factors including NTF3 and CDNF, and receptors such as GFRA1 and GFRA3, were downregulated and inversely associated with these parameters. Single-cell analyses revealed that neurotrophic factors are predominantly expressed by hepatic stellate cells, supporting their role as resident neuroglia-like cells in the liver. In another independent cohort, we observed a coordinated downregulation of NTF3 and sympathetic nerve markers in alcohol-associated hepatitis (AH), suggesting impaired NTF3-mediated neurotrophic support may contribute to sympathetic dysfunction in AH. Collectively, these findings uncover previously unrecognized neuro-regulatory dimensions in ALD and suggest that dysregulated autonomic and neurotrophic signaling may contribute to disease progression. Conflict of interestThe authors have declared that no conflict of interest exists.

bioinformatics↗

bioRxiv2026

An agentic AI environment to support biomedical research in collaborative academic environments

Agentic artificial intelligence (AAI) is increasingly used by biomedical scientists, where it has substantially lowered the difficulty of integrating computational, statistical and data-science approaches into day-to-day research activities, assisting with project design, analysis and manuscript preparation. Significant barriers remain, however, which are unlikely to be removed solely by releasing more capable AI models. Meaningful use still demands a technical fluency that many biomedical researchers lack: a PI and their lab members must learn how to use the AAI system, establish standard operating procedures (SOPs) for managing, sharing and curating data, and enforce rules that address data privacy and security. Existing commercial AAI systems, which were designed primarily for software engineering purposes, need to be significantly re-purposed for biomedical-related data science. We present Murmurent, shared software that sits beneath the agentic AI and provides the skills, procedures and protections to address the concerns above, removing the need for a lab to develop them independently. This includes (1) infrastructure to support projects and so-called choreographies} involving multiple group members; (2) a set of specialized agents each dedicated to typical biomedical data science tasks including software and statistical development, data visualization, literature search, equity, diversity, inclusion, and decolonization (EDID) review, and others; (3) a tiered memory which can retain important research decisions, intermediate, derived outputs and sensitive data, and which can exploit this information to automatically build better contexts in AAI sessions; (4) traceability records which are used by the AAI session to better plan and execute data analyses and software builds by, for example, helping to avoid repeating decisions that lead to dead-ends; (5) enforcement of SOPs for data maintenance and data governance across all lab members; and (6) multi-user capacity to allow groups to interact and collaborate. We use the system to identify putative inhibitors of Peptidyl-prolyl cis-trans Isomerase NIMA-interacting 1 (Pin1), a protein with a shallow catalytic site making it difficult to target. We describe the construction of several approaches to identify Pin1 inhibitors and the results they yield. Murmurent is open source.

bioinformatics↗

bioRxiv2026

MetaCarto: biologically faithful automatic layout for genome-scale metabolic maps

\textbf{Motivation:} Genome-scale metabolic reconstructions containing thousands of reactions are now curated and published for many organisms, but their visualization still relies heavily on manually constructed pathway maps. As these models grow in size and number, an automatic method is needed to organize their reactions into readable maps for visualization and downstream analysis.\\textbf{Results:} We developed \mytool, an automatic layout framework for genome-scale metabolic maps. \mytool identifies a biologically meaningful primary connection for each reaction and then organizes these connections into readable pathway-scale layouts, separating the biological representation of a reaction from its geometric placement. The resulting maps show strong agreement with curated KEGG pathway representations while maintaining geometric quality comparable to established graph-layout approaches. We applied \mytool to all 108 BiGG models and generated 2621 pathway maps without manual rearrangement. As a large-scale example, the human Recon3D reconstruction, containing 10\,600 reactions, was automatically decomposed into 93 maps and laid out in 107\,s. The generated maps are exported as Escher-compatible JSON and SVG files and can be directly browsed, edited, and used for metabolic data visualization.\\textbf{Availability and implementation:} Source code is available under CC BY 4.0 at \href{https://github.com/forxhunter/MetaCarto} {github.com/forxhunter/MetaCarto}. The complete collection of generated maps is available at \href{https://github.com/forxhunter/Awesome_visualization_Metabolic_Network} {GitHub map collection} and can be browsed interactively at \href{https://forxhunter.github.io/escher/} {forxhunter.github.io/escher}.\\textbf{Contact:} \href{mailto:tianyu16@illinois.edu}{tianyu16@illinois.edu}\\textbf{Supplementary information:} Supplementary data are available at \href{https://github.com/forxhunter/MetaCarto} {github.com/forxhunter/MetaCarto}.

bioinformatics↗

bioRxiv2026

Decoding the Transcriptome Dark Matter: Construction of Single-Cell Whole-Transcriptome Regulatory Atlas by dropTotal

To profile unknown ncRNAs-"dark matter" in single cells, we developed dropTotal, a high-throughput droplet-based total RNA-seq method that uses dU-modified GAT primer with temperature-ramp hybridization and droplet merge barcoding to co-detect coding and non-coding transcripts with record sensitivity (>13,500 genes/cell, including >2,000 lncRNAs and >500 sncRNAs), compatible with fresh, frozen, fixed, and FFPE tissues. Applied to ~75,000 human glioma nuclei, it captured 60,313 genes (18,681 lncRNA, 19,859 mRNAs and 6,753 sncRNAs), enabling ncRNA-driven regulatory landscape construction. In oligodendroglioma, module analysis identified recurrence-associated ncRNA-centered modules linked to therapy resistance and invasion; in glioblastoma, six cellular states showed hundreds of state-specific unannotated ncRNAs with divergent functions, from MIR222HG-mediated immune modulation to SCIRT-driven hypoxia adaptation. Alternative splicing analysis identified 428 state-specific junction markers and mapped cell-state-specific alternative splicing regulation. dropTotal offers broad application for decoding the underlying ncRNA biology and single-cell whole transcriptome regulatory mechanisms in cellular identity and disease progression.

genomics↗

bioRxiv2026

Enzymatic formation of a conserved isoaspartate in ribosomal protein uS11

Isoaspartate (isoAsp) formation is typically viewed as a "molecular clock" through nonenzymatic degradation of aspartate or asparagine during protein aging. Here we report a nearly universal enzymatic pathway for the formation of a conserved isoAsp in the bacterial ribosomal protein uS11. Proteome-wide protein-protein interaction scans using AlphaFold3 identified YbeY as a candidate enzyme from Escherichia coli. NMR spectroscopy supported a stable YbeY-uS11 complex from Thermotoga maritima. Biochemical assays indicated that EcYbeY catalysis is zinc-dependent and prefers the conserved Asn-Gly motif for isoAsp formation. A high-resolution cryo-electron microscopy structure of the 70S ribosome from E. coli {Delta}ybeY revealed that loss of isoAsp alters contacts with the 16S rRNA groove and bS21. Phylogenetic analysis indicated that YbeY is present in almost all bacteria, and its absence is correlated to changes in the Asn-Gly motif of uS11. Additionally, our structural analyses implicate Fap7 as the functional counterpart in archaea and eukaryotes.

biochemistry↗

bioRxiv2026

PlantAI: A Multi-Agent System for Plant Functional Genomics Analysis and Biological Knowledge Interpretation

Plant functional genomics requires the integration of sequence, expression, evolutionary, regulatory and literature evidence. However, the corresponding analyses are often distributed across disparate programs, scripts and databases, creating substantial barriers to task organization and result interpretation. Here, we present PlantAI, a multi-agent system that integrates bioinformatics analysis, project-level process tracking and knowledge-assisted interpretation. A Main Agent coordinates two complementary routes: an analysis route that invokes bioinformatics tools for RNA-seq and gene-family analyses, and a knowledge route that uses PlantAI-RAG for knowledge retrieval and evidence synthesis. PlantAI-RAG currently contains 31,207 plant-science literature records, comprising approximately 3.82 million normalized entities and 8.25 million literature-supported relation assertions. In an evaluation using plant-science questions, it achieved a Gold evidence-assertion recall of 86.7%, while strict accuracy ranged from 77% to 82% across three independent evaluator models. We further demonstrate an end-to-end task using 24 rice RNA-seq libraries collected under salt stress, spanning transcriptome analysis, candidate-family screening, HXK/HKL family analysis and knowledge-assisted interpretation, and prioritize OsHXK8 for experimental validation. By preserving analysis artifacts, run manifests, logs and environment records, PlantAI supports result verification and repeat execution while linking project-derived results to traceable literature evidence. Together, these capabilities provide an integrated and auditable framework to support plant functional genomics research.

bioinformatics↗

bioRxiv2026

ABISS: An Open-Source, Low-Cost Platform for Auditory and Visual Intrinsic Optical Signal Imaging

Defining the boundaries of functional cortical areas is increasingly important for targeted electro-physiology, optical imaging, viral delivery, and circuit manipulation. Intrinsic optical signal imaging (IOSI) provides a rapid and minimally invasive approach for mapping stimulus-evoked cortical activity, but its implementation often requires laboratory-specific combinations of stimulus-generation hardware, experiment-control software, synchronization devices, and data-acquisition systems. These requirements limit accessibility and hinder the use of IOSI as a routine functional mapping tool. Here, we present the Arduino-Based Intrinsic Stimulation System (ABISS), an open-source platform that integrates auditory and visual stimulus generation, trial timing, and image-acquisition triggering into a single programmable device. ABISS generates auditory tone stimuli, VGA-based visual stimuli, and tightly synchronized camera-trigger pulses without requiring a dedicated experiment-control system. Stimulus protocols are also fully modifiable in firmware. Performance was evaluated in auditory and visual cortices of mice. Engineering validation demonstrated accurate stimulus generation and synchronization between stimulus delivery and camera triggering over extended recording sessions. Biological validation showed that ABISS output results in auditory and visual intrinsic signal maps comparable to those obtained using highly specialized or commercial platforms. Together, these findings demonstrate the utility of a low-cost open-source platform for experimental control of intrinsic optical signal imaging. By reducing the technical and financial barriers associated with routine intrinsic optical imaging, ABISS facilitates broader adoption of functional cortical mapping as a tool for improved cortical localization in neuroscience experiments. Significance StatementFunctional cortical mapping is an increasingly important element of neuroscience experimental design as anatomical coordinates alone are often insufficient for defining cortical boundaries in individual animals. Intrinsic optical signal imaging provides an effective solution but traditionally requires specialized hardware, commercial stimulus-generation systems, and laboratory-specific synchronization workflows. We developed ABISS, an inexpensive, open-source platform that integrates auditory and visual stimulus generation with synchronized camera triggering in a single programmable device. ABISS produces functional cortical maps comparable to those obtainable with commercial or specialized systems while substantially reducing hardware complexity and cost. By making intrinsic optical signal imaging more accessible, ABISS lowers the practical barriers for routine functional mapping of the brain and promotes adoption of this important neuroscience technique.

neuroscience↗

bioRxiv2026

Protonation- and substrate-regulated dimer opening couples brain-type creatine kinase to vesicular and actin-remodeling membranes

Brain-type creatine kinase (CK-BB) buffers local ATP demand through reversible phosphotransfer between ATP and phosphocreatine, yet how this soluble metabolic enzyme engages membrane compartments is unknown. Here, we combine fluorescence microscopy, DEER spectroscopy, hydrogen-deuterium exchange and native mass spectrometry, DEER- and AlphaFold-guided modeling, and long-timescale molecular dynamics to define the pH- and substrate-regulated conformational landscape governing CK-BB membrane association. Acidification promotes curvature-sensitive membrane binding and redistributes endogenous and recombinant CK-BB from diffuse cytosolic pools to punctate vesicular structures and membrane ruffles. Substrates independently promote curvature-sensitive association at neutral pH. DEER and modeling reveal an asymmetric dimer in which the convex surface remains restrained, whereas the concave catalytic-regulatory surface samples pH- and substrate-dependent intermediates. We identify progressive dimer opening as a novel regulatory mechanism whereby acidification and substrate binding increase dynamics across the convex surface and N-terminal dimer interface, generating membrane-competent conformations that facilitate curvature sensing and membrane association. Substrate binding buffers acid-induced deprotection while preserving dynamics near the His191/Ser199 regulatory interface. These findings establish CK-BB as a previously unrecognized curvature-sensitive metabolic enzyme and define dimer dynamics as a molecular switch coupling protonation and substrate occupancy to curved-membrane recognition and localized ATP regeneration, with potential relevance to neurodegeneration and cellular stress.

biophysics↗

bioRxiv2026

ASOCompass: Context- and Chemistry-Aware Activity Prediction for Transferable Antisense Oligonucleotide Screening

Antisense oligonucleotide (ASO) activity is jointly influenced by nucleotide sequence, chemical modification, target-RNA context, dose, delivery protocol, and cellular environment. Most existing computational screening methods model only a subset of these factors, limiting their ability to predict experimentally measured activity across heterogeneous screening conditions and previously unseen biological contexts. We introduce ASOCompass, a context-and chemistry-aware framework for ASO activity prediction and candidate ranking. ASOCompass integrates contextualized ASO and target-RNA sequence representations with position-specific molecular representations of chemical modifications. It further incorporates dose and delivery information together with prototype-adapted transcriptomic representations of target genes and cell lines. To encourage chemically and biophysically informative representations, the model is jointly trained on auxiliary molecular-property and sequence-derived thermodynamic prediction tasks. We evaluate ASOCompass on ASO Atlas, a large patent-derived dataset of RNase H-mediated gapmer ASOs, under held-out drug, target-gene, cell line, and joint gene-cell line settings. ASOCompass achieves an overall Spearman correlation of 0.5970, improving over the strongest ASO-specific baseline by 0.0421, and consistently performs best across all four distribution shifts. When adapted to unseen SOD1 and KLKB1 targets, ASOCompass also provides more accurate candidate ranking across different annotation budgets, reaching correlations of 0.830 and 0.696 with 1,024 target-specific labels. Additional analyses suggest that molecular-property supervision improves modification-specific ranking, while the auxiliary thermodynamic task produces representations more closely aligned with measured inhibition. These results demonstrate the potential of jointly modeling sequence, chemistry, and experimental-biological context for transferable ASO screening.

bioinformatics↗

bioRxiv2026

Endotome as a Source of Human Peri-Aortic Brown Adipocytes

Brown adipocytes (BAs) hold therapeutic promise for obesity and metabolic diseases. While interscapular BAs derive from Pax3+/Myf5+ dermomyotome, peri-aortic BAs are inferred from an unknown Pax3+/Myf5- somitic origin. Here, we identify human endotome as an MYF5-independent source of peri-aortic BAs. Through interrogating public mouse organogenesis and in-house human trunk embryoid single-cell data, we show that the early endotome cells are MYF5-independent and are primed by TGF-{beta}-induced epithelial-to-mesenchymal transition. Mechanistically, endotome-to-BA specification requires sequential BMP inhibition and Wnt activation. This roadmap results in UCP1-expressing and metabolically active BAs that transcriptionally resemble in vivo peri-aortic BAT. The multipotent endotome cells also give rise to vascular smooth muscle and endothelial cells, offering a self-sufficient source for BAT vasculature. Endotome-derived BAs show accelerated differentiation, reduced heterogeneity, and sustained Wnt activity. Thus, the endotome provides a versatile platform for generating BAs and supporting vasculature, with implications for cell-based therapy and tissue engineering in metabolic disease.

developmental biology↗

bioRxiv2026

NeuroEnergetics-on-Chip: a novel 3-compartment microfluidic platform to study metabolic interactions between brain parenchyma and cerebral vasculature

Neurological disorders are a major cause of death and disability worldwide. The brains energy metabolism is essential to its proper function, yet the mechanisms driving neuroenergetic dysfunction remain poorly understood. A key challenge is the limited availability of human-relevant models that can reproduce the complexity of brain physiology. An Organ-on-Chip (OoC) system was developed to mimic the neurovascular unit metabolic coupling by incorporating human isogenic iPSC-derived endothelial-like cells, pericyte-like cells, astrocytes, and a cerebral organoid, representing the main cellular components of the NVU. The novel, customized microfluidic platform enables research on neurovascular coupling by interconnecting a blood-brain barrier-on-a-chip model with a 3D brain parenchymal compartment to mimic physiological conditions. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/733618v1_ufig1.gif" ALT="Figure 1"> View larger version (75K): org.highwire.dtl.DTLVardef@9fc9f3org.highwire.dtl.DTLVardef@838a7corg.highwire.dtl.DTLVardef@1f8df76org.highwire.dtl.DTLVardef@16ef40_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

OryzaG3: A Single-species Genomic Foundation Model Pretrained on Rice Pangenome

While multi-species genomic language models have advanced biological representation learning, high-quality, single-species foundation models for crops remain scarce. Leveraging recently expanded rice pangenome resources, we introduce OryzaG3, a species-specific DNA language model with 700M parameters. OryzaG3 was pretrained on 59.20 Gb of chromosome-level sequences from 149 high-quality rice genomes using a non-overlapping 3-mer tokenization strategy and a causal language modeling objective, featuring context-length variants up to 32k tokens. On the Plants Genomic Benchmark polyA prediction task, OryzaG3 achieves competitive predictive performance against leading multi-species models while delivering a four-fold increase in inference throughput under identical long-context conditions. Ultimately, OryzaG3 demonstrates that lightweight, single-species foundation models trained on high-quality pangenomes can match multi-species benchmarks while significantly reducing computational overhead. This work provides a scalable framework for rice functional genomics, molecular breeding, and targeted crop foundation model development.

bioinformatics↗

bioRxiv2026

Proton-coupled alternating access in a versatile Spns drug efflux pump from Mycobacterium smegmatis

Spns transporters are a mechanistically distinct branch of the major facilitator superfamily that regulate lipid transport, lysosomal homeostasis, immunity and disease. How the conserved Spns fold integrates protonation, substrate binding and alternating access to support chemically and directionally diverse transport remains unresolved. Here we combine DEER spectroscopy in lipid nanodiscs with DEER-and AlphaFold-guided modeling and protonation-mimetic mutagenesis to define the conformational landscape of the Mycobacterium smegmatis homolog MsSpns. Protonation shifts MsSpns toward an inward-facing state, whereas deprotonation favors a broader outward-facing ensemble through remodeling of intracellular and extracellular gates. Protonation-mimetic substitutions identify Glu126 as a switch that stabilizes an inward-facing, substrate-entry-competent conformation, while Asp38 and Asp57 favor outward-facing states and tune the extracellular proton-sensing network. The substrate-binding cavity displays distinct proton sensitivity and weaker cooperativity than gating networks. Hydrophilic cationic substrates stabilize the outward-facing state, consistent with efflux antiport, whereas lipophilic compounds favor the inward-facing state, suggesting uptake or allosteric stabilization. Thus, conserved proton-coupling elements can power opposing transport modes, revealing the mechanistic versatility of the Spns fold and its therapeutic potential.

biophysics↗

bioRxiv2026

Integrative taxonomy of Trichiurus (Scombriformes: Trichiuridae) reveals a new cutlassfish species from Java, Indonesia

The genus Trichiurus is the most economically valuable fish in the family Trichiuridae, currently recognized to include 10 valid species. However, historically numerous morphologically similar congeners have been erroneously assigned as synonyms or subspecies of T. lepturus. In this study, we examined 16 hairtail specimens collected from the southern waters of Java Island, Indonesia. Integrated morphological and mitochondrial phylogenetic analyses (COX1 and 16S rRNA), compared against global Trichiurus sequences, revealed that these specimens form an independent lineage that diverged early from other congeners. Consequently, we describe this lineage as a previously undescribed cryptic species. Diagnostic characters include: first anal-fin spine below 36th-37th dorsal-fin rays; anus below 35th-36th dorsal-fin rays; anteriormost tip of supraoccipital well posterior to posterior distal margin of eye; anterior margin of the pectoral-fin spine non-serrated; fangs on both jaws with barb-like processes; upper jaw long, mean 16.6% (15.5-17.6%) of preanal length; snout short, 12.0% (10.9-13.1%) of preanal length; eye small, diameter 5.3% (4.3-5.7%) of preanal length; and absence of hyperostosis on dorsal cranium. We herein propose the name Trichiurus javaensis sp. nov., and provide a formal morphological description and diagnostic characterization of this species.

zoology↗