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Biology subjects

Ruan, J.

Publications and source records attributed to Ruan, J..

At least 19 recordsLinked to original sources

Milankovic cycles and Cultural Evolution as Important Catalysts for Hominin Genetic Diversification

Climate variability is widely considered a key driver of human evolution, yet the mechanisms linking long-term climate change driven by Milankovi[c] cycles to hominin demography and genetic diversity remain elusive. Here we couple an agent-based demographic model, incorporating an idealized genetic marker, cultural dynamics, and a realistic Pleistocene climate framework, to quantify how astronomically forced climate and vegetation variability shaped the genetic structure of African hominins over the past 1.9 Myr. We show that warm early Pleistocene climates sustained a continent-wide network of genetically diverse demes until ~900 ka. The subsequent decline in atmospheric CO2, associated cooling, and reduced vegetation during the Mid-Pleistocene Transition triggered widespread demographic collapse, with populations surviving only in southern and eastern Africa. This reorganization in population structure leads to a decline in simulated genetic diversity, consistent in timing with genomic and archeological evidence. Introducing cultural innovations in the model, represented as enhanced carrying capacity, enables hominin populations to recover from this diversity bottleneck, adapt to increasingly harsh late Pleistocene environments and long glacial periods, rapidly expand across Africa during interglacials, and ultimately disperse into Eurasia. Our results identify Milankovi[c]-scale climate forcing and cultural growth as important catalysts of hominin population structure and genetic diversification.

evolutionary biology↗

PanSVmerger: a flexible pipeline for merging multiallelic structural variants in pangenome graphs

SummaryPangenome graphs capture extensive genetic diversity but introduce analytical challenges due to the redundant representation of structural variations (SVs). While existing tools effectively address cross-sample redundancy or cross-locus redundancy, none specifically target the intra-locus allelic redundancy inherent to pangenome graphs. Here, we present PanSVmerger, an open-source tool designed to consolidate redundant multiallelic SVs within individual loci using three complementary clustering strategies: adaptive k-mer-based Jaccard distance, global alignment distance via VSEARCH, and length distribution. Validation on HPRC pangenome data demonstrates that PanSVmerger effectively reduces multiallelic complexity (e.g., AC [≥] 3 loci from 62.4% to 4.7% using Strategy A) with a modest trade-off: Recall decreased from 97.13% to 93.58%, while precision improved from 94.95% to 96.56%, yielding an overall F1-score of 95.05%. These results demonstrate that PanSVmerger effectively consolidates redundant allele representations with only a minimal loss of sensitivity, making it well-suited for downstream applications that require clean, non-redundant variants. Availability and implementationPanSVmerger is implemented in Python 3.8+ and freely available under the MIT license at GitHub: https://github.com/tingting100/PanSVmerger. The software requires vcflib, bcftools, and optionally VSEARCH. Comprehensive documentation and tutorials are provided.

bioinformatics↗

Super-Resolved Single Small Extracellular Vesicle Assay enabled by a Plasmonic Nanohole Array

The accurate quantification of biological nanoparticles, such as small extracellular vesicles (sEVs), is fundamentally hindered by a resolution-coincidence trade-off in digital assays. While physical confinement can isolate single particles, conventional optical readouts remain diffraction-limited, causing multi-particle occupancy to be miscounted as single events and thereby restricting the analytical dynamic range. Here, we report a nanoplasmonic platform that overcomes this limit by introducing a geometry-defined interface that uniquely unifies nanoscale compartmentalisation and near-field-assisted super-resolution imaging. Utilising a gold plasmonic nanohole array, the strict geometric periodicity of the lattice simultaneously serves as a template for single-vesicle confinement and a deterministic grid that generates an array of localised surface plasmon resonance near-field hotspots. This position-deterministic illumination pattern imposes known geometric priors on the excitation field, shifting high-spatial-frequency information into the detectable bandwidth to achieve sub-100 nm lateral resolution. This dual-purpose geometric determinism enables high-fidelity digital readout of individual vesicles with significantly fewer sub-images than stochastic, speckle-based metasurface structured illumination microscopy approaches. The assay achieves an analytical limit of detection of 143 sEVs/{micro}L, matching the performance of state-of-the-art single-EV counting technologies. It successfully differentiates distinct sEV subpopulations based on surface biomarker expression, establishing a clear pathway for future clinical liquid biopsy applications. By replacing stochastic loading and illumination with geometric design, this work establishes a robust framework for precise vesicle interrogation with broad implications for emerging translational applications and fundamental biology.

bioengineering↗

Engineering a Novel Bacterial Encapsulin for Programmable Surface Functionalization: From Single-Target to Mosaic Nanovaccines

Encapsulins are prokaryotic self-assembling protein nanocages with promise as nanovaccine scaffolds. Their utility as modular platforms require tolerance to surface engineering, high-yield soluble production, formulation stability, and controlled antigen (co-)display. Herein, a previously uncharacterized encapsulin from Alkaliphilus metalliredigens is engineered into a SpyCatcher-decorated nanoscaffold (Am-S) that enables controlled surface display of SpyTagged antigens. Cryo-EM confirms that the native encapsulin forms a T = 1 icosahedral nanocage, and that C-terminal SpyCatcher fusion yields Am-S without compromising nanocage assembly, symmetry, or structural integrity. Notably, Am-S exhibits high-yield soluble production in Escherichia coli, remains monodisperse after freeze-thaw and extended storage, and supports efficient SpyTagged peptide conjugation for single- and multi-antigen display. As a proof-of-concept, Am-S is functionalized with Alzheimers disease-associated amyloid-{beta} and/or hyperphosphorylated tau epitopes to generate single-target nanocages displaying either antigen and dual-target mosaic nanocages co-displaying both. In mice, Am-S antigen display enhances antigen-specific IgG responses relative to free antigens and induces predominantly IgG1-biased humoral immunity. Mosaic nanocages elicit antibodies against both targets, with immune sera selectively recognizing amyloid-{beta}- and phosphorylated tau-associated pathology in ex vivo brain sections from Alzheimers disease mouse models. These findings position Am-S as a manufacturable scaffold for developing multi-targeting nanovaccines against complex diseases.

synthetic biology↗

Widespread use of invalid statistical tests in biomedical machine learning

Cross-validation is routinely used to compare performance in biomedical artificial intelligence. Standard tests ignore correlation across cross-validation folds, inflating false-positive rates. In a PRISMA-guided meta-analysis of 184 studies (impact factor [≥] 15) across 30 biomedical fields, 97% use invalid tests. Among studies with abstract-level claims supported by invalid tests, 59% rely on a spurious comparison: one that loses significance after correcting for this correlation. On average, regaining significance requires a 43% larger effect. Extending these findings to the broader literature, we estimate that spurious comparisons occur in nearly two in three studies and support abstract-level claims in nearly one in three studies. Simulations confirm false-positive rates paradoxically approach 100% when cross-validation is repeated to improve stability. We introduce SHARP, a redesign of cross-validation, which best balances false-positive control and power among 13 benchmarked tests. These results reveal widespread fragility in biomedical artificial intelligence and offer a practical route to valid comparisons.

bioinformatics↗

Autoluminescence characteristics of 25 Phalaenopsis orchids following transient transformation with eFBP2

Engineering autoluminescent plants, especially horticultural crops, has recently emerged as a promising research area, with one current approach involving the transgenic introduction of fungal bioluminescence pathway genes. Although autoluminescent plants such as tobacco and petunia have been created, it remains unclear whether all horticultural plants have the potential to be autoluminescent after genetic modification, especially those having flowers with dark colors and thick cuticles. To understand whether, and what if any, floral traits affect autoluminescence potential, we assess the autoluminescence characteristics of 25 representative Phalaenopsis cultivars after transient transformation of fungal bioluminescence pathway genes, alongside several key morphological and biochemical traits. Our results demonstrate that autoluminescence characteristics are correlated with floral color lightness, organ textures and epidermal cell types. In contrast, the content of the substrates of luciferin--caffeic acid and tyrosine, and the infiltration ease of inoculation solution into floral organs after injection, have limited effects on autoluminescence characteristics. Autoluminescence intensity can be reasonably predicted using five floral traits investigated, as 80.4% of variation can be explained by these traits. Our study not only identifies specific Phalaenopsis cultivars with high potential for developing autoluminescent lines but also provides a selection framework applicable to other horticultural crops.

plant biology↗

Hyperactivated YAP1 Drives an Invasive EMT Subtype of Cervical Squamous Cell Carcinoma

Cervical cancer (CVC) is classically understood as an HPV-driven disease in which high-risk HPV infects cervical basal epithelial cells, induces neoplastic transformation, and drives upward epithelial expansion, pathogenic events underlying the success of cytology- and HPV-based screening. With widespread HPV vaccination and screening, the WHO has launched the CVC elimination initiative and believes that CVC will be the first cancer that would be eliminated as a public health problem. However, statistics showed that CVC remains the most common gynecologic malignancy worldwide, and in the United States, where HPV testing and Pap smears have reached near-maximal implementation, the CVC mortality rate has plateaued for more than two decades. These epidemiologic trends suggest the existence of a subset of CVC that can escape current screening strategies. Here, we demonstrate that hyperactivation of YAP1 caused by disruption of Hippo-YAP signaling is sufficient to induce a subtype of HPV-independent invasive CVC that lacks surface lesions and therefore evades HPV- and cytology-based detection. Using single-cell RNA sequencing combined with high-resolution spatial transcriptomics, we define the cellular architecture, molecular pathways, and immune microenvironment underlying this invasive subtype. We show that YAP1-driven tumors adopt an EMT-high transcriptional state and selectively recruit immunosuppressive myeloid-derived suppressor cells that functionally interact with cancer cells to promote invasion and progression. Our findings suggest that targeting the disrupted Hippo signaling may offer a new strategy to prevent the subset of invasive CVC that current HPV- and Pap-based programs cannot detect, an essential step toward achieving global CVC elimination.

cancer biology↗

Rete Ovarii Epithelial Cells as an Unappreciated Cell of Origin for Pelvic and Ovarian High-Grade Serous Carcinoma

Over the past two decades, converging clinicopathologic, molecular, and evolutionary evidence has established that pelvic and ovarian high-grade serous carcinoma (HGSC) originates predominantly from tubal-type epithelia rather than the ovarian surface epithelium. Consequently, Fallopian tube secretory epithelial cells are widely recognized as the principal cell of origin for HGSC. However, the female reproductive tract contains additional tubular epithelial networks whose potential contributions to HGSC pathogenesis remain unexplored. Here, we identify the rete ovarii (RO), a complex network of intra- and extra-ovarian tubules located within the ovarian hilus and mesovarium, as an alternative candidate tissue of origin for HGSC. We demonstrate that genetic and genomic alterations in rete ovarii epithelial cells (ROECs) can drive their malignant transformation, giving rise to tumors that closely recapitulate the histologic and molecular characteristics of human HGSC. Spatially resolved single-cell transcriptomic analyses of tumors derived from Brca/Trp53/Pten-deficient ROECs (BTP-RO) reveal distinct invasive and immunosuppressive molecular programs. These findings establish ROECs as a previously unrecognized cell of origin for HGSC, expanding the landscape of potential precursor populations beyond the Fallopian tube. The RO-based HGSC model provides a powerful framework for developing origin-informed prevention strategies, early detection approaches, and targeted therapeutics.

cancer biology↗

A Rapid and Highly Sensitive CRISPR Assay Utilizing Cas12a Orthologs for the Detection of Novel Duck Reovirus

The novel duck reovirus (NDRV) disease presents a significant threat to the poultry industry due to the absence of effective therapeutic measures. As a result, there is an urgent need to develop innovative rapid diagnostic methods for early virus detection. In this study, we developed a Rapid Visual CRISPR Assay to detect the NDRV S3 gene using novel Cas12a orthologs. Specifically, we compared the performance of two candidates, Gs12-16 and Gs12-18, in detecting the NDRV S3 gene to identify a highly sensitive and efficient CRISPR-based diagnostic method. Our results demonstrated that both Gs12-16 and Gs12-18 exhibited strong cis- and trans-cleavage activities for classical "TTTV" protospacer adjacent motif (PAM)-containing targets in vitro, although they required different reaction temperatures. Notably, Gs12-18 showed relatively higher activity for dsDNA targets compared to Gs12-16, indicating that Gs12-18 is more suitable for CRISPR-based nucleic acid detection applications. To leverage these properties, we integrated Gs12-18 with loop-mediated isothermal amplification (LAMP) technology to establish a LAMP-CRISPR/Gs12-18-mediated method for detecting the NDRV S3 gene. This approach enables highly sensitive and visually detectable on-site identification of the NDRV S3 gene, achieving a sensitivity of 38 copies per reaction. Our LAMP-CRISPR/Gs12-18-based method can be utilized for highly sensitive detection of NDRV nucleic acids.

synthetic biology↗

Unanchored ubiquitin chains promote the non-canonical inflammasome via UBXN1

Ubiquitination is a major posttranslational covalent modification that regulates numerous cellular processes including inflammasome signaling. Cells also contain unanchored ubiquitin chains (polyUb) that bind protein targets non-covalently, but their physiological functions in immunity have been appreciated only recently. Here, we report that ubiquitin regulatory x domain-containing protein 1 (UBXN1) activates the noncanonical inflammasome via unanchored Lysin (K) 48- or 63-linked polyUb. UBXN1 deficiency impairs the activation of caspase-4/11, secretion of inflammasome-dependent cytokines and pyroptosis in response to intracellular lipopolysaccharide (LPS). UBXN1-deficient mice are protected from LPS- and cecal-ligation-and-puncture-induced sepsis, evidenced by reduced mortality and systemic inflammation, compared to UBXN1-sufficient littermates. Mechanistically, UBXN1 together with unanchored K48/63-linked polyUb bind caspase-4/11, the intracellular sensors of LPS, and promote their assembly and activation. Depleting cellular unanchored polyUb with recombinant ubiquitin-specific proteinase 5 (USP5) reduces UBXN1 binding to caspase-4/11 and inflammasome signaling, while USP5 inhibitors enhance pyroptosis in an UBXN1-dependent manner. Thus, this study identifies a critical UBXN1-dependent posttranslational mechanism involved in noncanonical inflammasome activation and UBXN1 as a potential therapeutic target for sepsis and advances a fundamental understanding of unanchored polyUb biology.

immunology↗

Synaptic vesicle endocytosis deficits underlie GBA-linked cognitive dysfunction in Parkinson's disease and Dementia with Lewy bodies

GBA is the major risk gene for Parkinsons disease (PD) and Dementia with Lewy Bodies (DLB), two common -synucleinopathies with cognitive deficits. We investigated the role of mutant GBA in cognitive decline by utilizing Gba (L444P) mutant, SNCA transgenic (tg), and Gba-SNCA double mutant mice. Notably, Gba mutant mice showed early cognitive deficits but lacked PD-like motor deficits or -synuclein pathology. Conversely, SNCA tg mice displayed age-related motor deficits, without cognitive abnormalities. Gba-SNCA mice exhibited both cognitive decline and exacerbated motor deficits, accompanied by greater cortical phospho--synuclein pathology, especially in layer 5 neurons. Single-nucleus RNA sequencing of the cortex uncovered synaptic vesicle (SV) endocytosis defects in excitatory neurons of Gba mutant and Gba-SNCA mice, via robust downregulation of genes regulating SV cycle and synapse assembly. Immunohistochemistry and electron microscopy validated these findings. Our results indicate that Gba mutations, while exacerbating pre-existing -synuclein aggregation and PD-like motor deficits, contribute to cognitive deficits through -synuclein-independent mechanisms, involving dysfunction in SV endocytosis.

neuroscience↗

LPS binding caspase activation and recruitment domains (CARDs) are bipartite lipid binding modules

Caspase-11 is an innate immune pattern recognition receptor (PRR) that detects cytosolic bacterial lipopolysaccharides (LPS) through its caspase activation and recruitment domain (CARD), triggering inflammatory cell death known as pyroptosis. Caspase-11 also detects eukaryotic (i.e. self) lipids. This observation raises the question of whether common or distinct mechanisms govern the interactions with self and nonself lipids. In this study, using biochemical, computational, and cell-based assays, we report that the caspase-11 CARD functions as a bipartite lipid-binding module. Distinct regions within the CARD bind to phosphate groups and long acyl chains of self and nonself lipids. Self-lipid binding capability is conserved across numerous caspase-11 homologs and orthologs. The symmetry in self and nonself lipid detection mechanisms enabled us to engineer an LPS-binding domain de novo, using an ancestral CARD-like domain present in the fish Amphilophus citrinellus. These findings offer critical insights into the molecular basis of LPS recognition by caspase-11 and highlight the fundamental and likely inseparable relationship between self and nonself discrimination.

immunology↗

RO8191, a new compound for initiating embryoimplantation in mice

During early pregnancy in mice, leukemia inhibitory factor (LIF) regulates embryo implantation by activating the JAK/STAT3 signaling pathway. The STAT3 pathway has been recognized to play a critical role in embryo implantation. However, it is not clear whether STAT3 activation itself can cause induction of embryo implantation. In this study, the effects of RO8191, a potential STAT3 activator, on embryo implantation were investigated through a series of studies with different mouse models. We found that the injection of RO8191 can induce embryo implantation by activating the STAT3 pathway in delayed implantation mice. Furthermore, RO8191 can initiate decidualization, which is essential for embryo implantation, in uterine epithelial-specific Stat3, Gp130, or Lifr conditional knockout (cKO) mice, which shows infertility due to embryo implantation failure. Histomorphological observations revealed that successful embryo implantation and embryonic development was seen in Lifr cKO mice. Increased epithelial detachment and vascularization were observed in Stat3 cKO mice, and excessive inflammatory response and embryo death were observed in Gp130 cKO mice. These results suggest that STAT3, Gp130 and LIFR each play a distinct role in embryo implantation and development. Although the specific mechanisms of RO8191 are not fully understood, the present study will provide insights to support the application of RO8191 in treating recuurent implantation failure.

developmental biology↗

Expanding the CRISPR toolbox by engineering Cas12a orthologs of metagenomic discovery

Cas12a (Cpf1) is a CRISPR-associated nuclease with broad utility in genome editing and molecular diagnostic applications. However, the widespread adoption of CRISPR-Cas12a nucleases and their variants has been hindered by the requirement for a specific protospacer adjacent motif (PAM), relatively low CRISPR RNA (crRNA) activity and the inability to multiplex nucleic acid detection alone. To overcome these limitations, we employed a comprehensive framework combined with AlphaFold2 to de novo mine 1,261 previously unexploited Cas12a orthologs from the global microbiome. Following experimental analysis, we identified the most promising 21 Cas12a nuclease orthologs and designated them "Genie scissor 12" (Gs12). Our analysis uncovered two exceptional variants among these newly identified orthologs: Gs12-10, a first natural PAM-less Cas12a ortholog, which can recognize 52 distinct PAM types, representing a significant 1.8-fold expansion in recognition range compared to the relative LbCas12a PAM; and Gs12-7MAX, an engineered variant of Gs12-7 that exhibited 1.27-fold higher editing efficiency than enAsCas12a-HF. Furthermore, we harnessed Gs12-1, Gs12-4, Gs12-9, and Gs12-18, along with their corresponding engineered crRNAs, to develop a powerful four-channel multiplexed CRISPR-based nucleic acid detection system. The discovery of diverse functions in Cas12a offers a deeper understanding of the CRISPR/Cas12a family. Also, it holds great promise for expanding its applications and uncovering the untapped potential of other CRISPR/Cas systems. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=189 SRC="FIGDIR/small/615316v1_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@bee75forg.highwire.dtl.DTLVardef@1480f61org.highwire.dtl.DTLVardef@1e9cbc9org.highwire.dtl.DTLVardef@4211b2_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

TSTA: Thread and SIMD-Based Trapezoidal Pairwise/Multiple Sequence Alignment Method

AbstractsThe rapid advancements in sequencing length necessitate the adoption of increasingly efficient sequence alignment algorithms. The Needleman-Wunsch method introduces the foundational dynamic programming (DP) matrix calculation for global alignment, which evaluates the overall alignment of sequences. However, this method is known to be highly time-consuming. The proposed TSTA algorithm leverages both vector-level and thread-level parallelism to accelerate pairwise and multiple sequence alignments. Availability & ImplementationSource code are available at https://github.com/bxskdh/TSTA.

bioinformatics↗

CetZ1-dependent assembly and positioning of the motility machinery in haloarchaea

The archaeal tubulin-like cytoskeletal protein CetZ1 is required for rod-cell morphogenesis during the development of motility in Haloferax volcanii. This is expected to improve swimming speed and directionality. Here, we found that deletion of cetZ1 or expression of a GTPase-defective mutant caused a substantial defect in the assembly of the motility machinery, including the archaellum base marker protein ArlD1, the chemotaxis sensory array adapter CheW1, and signal transducer CheY. Furthermore, overexpression of cetZ1 reduced the assembly and polar placement of the motility machinery without detectably affecting the rod shape of motile cells. In contrast, deletion of the conserved paralog cetZ2 caused no defects in swimming or rod shape, although expression of the cetZ2 GTPase-defective mutant reduced motility whereas cetZ2 overexpression caused mild hyper-motility; these effects were dependent on the presence of cetZ1. A functional CetZ1-mTq2 fusion strongly localized at the poles of mature motile cells, where it partially co-localized with the motility machinery markers. These results suggest that CetZ1 has another role in the organisation or structure of the cell poles that promotes the assembly of the motility machinery. The multiple roles and locations of CetZ1 during motile cell development are reminiscent of the multiple functions of eukaryotic cytoskeletal proteins.

microbiology↗

MIPDB: A maize image-phenotype database with multi-angle and multi-time characteristics

Plant phenomics has become one of the most significant scientific fields in recent years. However, typical phenotyping procedures have low accuracy, low throughput, and are labor-intensive and time-consuming. Large-scale phenotypic collection equipment, on the other hand, is pricy, rigid, and inconvenient. The advancement of phenomics has been hampered by these restrictions. Lightweight picture collection equipment can now be used to capture plant phenotypic data thanks to the development of deep learning-based image identification. For the purpose of training the model, this approach needs high-quality annotated datasets. In this study, we used a handheld camera to gather multi-angle, multi-time series images and an unmanned aerial vehicle (UAV) to create a maize image phenotyping database (MIPDB). Over 30,000 high-resolution photos are available in the MIPDB, with 17,631 of those images having been carefully tagged with point-line method. The MIPDB can be accessed by the general public at http://phenomics.agis.org.cn. We anticipate that the availability of this superior dataset will stimulate a new revolution in crop breeding and advance deep learning-based phenomics research.

plant biology↗

Molecular basis for the assembly of the Vps5-Vps17 SNX-BAR proteins with Retromer

Retromer mediates endosomal retrieval of transmembrane proteins in all eukaryotes and was first discovered in yeast in complex with the Vps5 and Vps17 sorting nexins (SNXs). Cryoelectron tomography (cryoET) studies of Retromer-Vps5 revealed a pseudo-helical coat on membrane tubules where dimers of the Vps26 subunit bind Vps5 membrane-proximal domains. However, the Vps29 subunit is also required for Vps5-Vps17 association despite being far from the membrane. Here, we show that Vps5 binds both Vps29 and Vps35 subunits through its unstructured N-terminal domain. A Pro-Leu (PL) motif in Vps5 binds Vps29 and is required for association with Retromer on membrane tubules in vitro, and for the proper recycling of the Vps10 cargo in Saccharomyces cerevisiae. CryoET of Retromer tubules with Vps5-Vps17 heterodimers show a similar architecture to the coat with Vps5-Vps5 homodimers, however, the spatial relationship between Retromer units is highly restricted, likely due to more limited orientations for docking. These results provide new mechanistic insights into how Retromer and SNX-BAR association has evolved across species.

cell biology↗