Biology subjects

Cao, M.

Publications and source records attributed to Cao, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

CRISPR-Cas9 based Mutagenesis in the Entomopathogenic Nematode Steinernema hermaphroditum and the Maintenance of Mutant Lines

Entomopathogenic nematodes (EPNs) from the genus Steinernema and Heterorhabditis form mutualistic relationships with symbiotic bacteria from the genus Xenorhabdus and Photorhabdus, respectively. Together, these nematode-bacterium pairs infect and kill insect hosts--primarily larvae from the orders Lepidoptera and Coleoptera. This tripartite interaction provides a powerful model for investigating the molecular mechanisms underlying mutualism and parasitism. A key step toward this goal is the development of a genetically tractable EPN. While RNAi has been applied in some EPN species, stable, transgenerational genetic tools remain limited. Here, we establish a robust CRISPR-Cas9 system in the emerging model Steinernema hermaphroditum, a species that is easily cultivated in both in vivo and in vitro conditions and amenable to gonadal microinjection. Notably, its hermaphroditic reproduction simplifies the generation of genetically stable mutant lines. We present a detailed protocol for efficient, targeted gene knockout via microinjection in S. hermaphroditum. As a proof-of-concept, we knocked out a conserved homologue, unc-22, which causes a twitching phenotype. The CRISPR-Cas9 based genome editing in S. hermaphroditum has potential to be used to express transgene, or to be adapted to other EPN species that are applicable to benefit agriculture. SUMMARYThis article demonstrates CRISPR-Cas9 mediated genome engineering in Steinernema hermaphroditum, an entomopathogenic (EPN: insect-parasitic) nematode and an emerging genetic model. The described technology is useful for creating mutants allowing for the elucidation of gene functions in the nematode biology that is relevant to mutualistic and parasitic symbiosis.

genetics↗

bioRxiv2025

PhysioMotion Artifact: A Task-Driven EEG Dataset with Channel-Level Motion Artifact Annotations

Physiological artifacts pose persistent challenges in electroencephalo-gram (EEG) data acquisition, often compromising interpretation and post-analysis of EEG signals across research and clinical applications. To address such limitations, including various artifact types, insufficient annotations, and low spatial resolutions, we present PhysioMotion Artifact, a large-scale, task-driven EEG dataset with channel-level artifact annotations. EEG data was acquired from 30 healthy participants performing 16 systematically designed single-type and multi-type movement tasks, inducing 14 distinct types of physiological artifacts. To demonstrate the utility of the dataset, we implemented a Convolutional Neural Networks-Transformer hybrid model for artifact detection and classification, achieving 98% accuracy in binary classification and 85% in 14-class classification tasks.

neuroscience↗

bioRxiv2025

Time-Resolved Mapping in Calves Reveals BoHV-1 Shift From Mucosal Replication to Trigeminal Neuroinvasion and IFN-α-bPML Antagonism

Bovine herpesvirus 1 (BoHV-1) causes huge cattle losses, yet the transition from mucosal replication to neuroinvasion is poorly resolved. Using a controlled calf model, we integrated quantitative virology and transcriptomics to map pathogenesis and define the role of promyelocytic leukemia protein (PML). Calves inoculated intranasally/ocularly (1.4x10^6 pfu/head) were sampled daily (1-14 dpi) for gB-qPCR; tissues at 4 and 14 dpi were analyzed for viral DNA and trigeminal ganglia (TG) mRNA-seq. Shedding peaked at 3-6 dpi (nasal > ocular >> rectal) and declined by 10-14 dpi. Tonsils bore the highest burden at 4 dpi; TG was low-positive at 4 dpi but remained positive at 14 dpi, indicating neuroinvasion. TG programs shifted from early proteostasis priming (4 dpi) to immune/ECM activation with synaptic repression (14 dpi). In MDBK/Vero cells, IFN- increased bovine PML (bPML) and enlarged PML nuclear bodies (PML-NBs), reducing very-early viral DNA, whereas BoHV-1 disrupted PML-NB integrity. bPML isoforms diverged (bPML1/6 pro-viral; bPML3/4/5 antiviral). Cross-species STRING mapped a conserved PML-SUMO1-UBE2I-DAXX-SP100 core. These data delineate the mucosal-to-neuronal trajectory, establish PML as both effector and viral target, and nominate SUMO/ubiquitin-linked proteostasis as a tractable antiviral leverage point.

microbiology↗

bioRxiv2025

An evolutionary leap in plant reproduction: From archegonia and motile sperm to embryo sacs and pollen tubes

The transition of plants from water to land marks a pivotal step in their evolutionary history, with the change in reproductive mode being the most fundamental. This change freed plant reproduction from aquatic dependence, fostering terrestrial lifes prosperity. Key to the shift from archegonial to embryo sac reproduction are pollen tube emergence and female gametophyte changes, though their evolutionary trajectories and mechanisms remain unclear. Ginkgo, a basal gymnosperm, occupies a pivotal position in this transition, retaining motile sperm, simplified archegonia, and primitive pollen tubes, making it an ideal model. To study how the transition between these two reproductive modes occurred, we collected transcriptome data from the reproductive organs of Ginkgo and evolutionarily representative species. Our findings reveal the MYB98-CRP-ECS module- critical for angiosperm pollen tube guidance--in Ginkgos mature archegonia, with pollen tubes containing guidance components. While egg cells are transcriptionally and functionally conserved across land plants, changes in the cell fate of other female gametophyte component cells drove the shift from archegonia to embryo sacs. Pollen tubes may originate from fern male gametophyte internalization and modification. These findings clarify the evolutionary path and molecular basis of this major reproductive transition.

plant biology↗

bioRxiv2025

CRISPR-Cas9 gene editing in the agriculturally beneficial entomopathogenic nematode Steinernema feltiae

The entomopathogenic nematodes (EPN) of the genus Steinernema serves as a valuable experimental model for studying microbial symbiosis and is economically important as organic pest control agent in agriculture. Although most Steinernema species are dioecious (male-female), consistent genetic manipulation has thus far only been demonstrated in the hermaphroditic species Steinernema hermaphroditum. In this study, we adapted a CRISPR-Cas9-based gene editing approach to Steinernema feltiae, a dioecious species widely used in agricultural applications. Using gonadal microinjection, we targeted the conserved gene unc-22 in S. feltiae and generated stable mutant lines with large on-target deletions. Mating tests revealed that Sf-unc-22 is X-linked and exhibits a conditionally dominant twitching phenotype. Additionally, Sf-unc-22 mutants display distinct body morphology compared to wild-type nematodes. Homozygous mutant lines can be reliably maintained through cryopreservation. Altogether, our work provides a proof of concept that genetic tools developed in S. hermaphroditum can be effectively adapted to other agriculturally relevant and dioecious Steinernema species-- broadening the scope of molecular genetic research in microbial ecology and enhancing their potential applications in agriculture.

genetics↗

bioRxiv2025

Association of E. coli Nissle with insect-parasitic nematode Steinernema hermaphroditum

Steinernema species are soil-dwelling and insect-parasitic nematodes that associate with symbiotic Xenorhabdus bacteria. During the infective juvenile (IJ) stage, Steinernema nematodes package species-specific Xenorhabdus bacteria in the anterior intestinal pockets. The nematodes can survive in the soil for months as they seek insect prey. The mechanisms of how these nematodes associate with environmental microbes other than their Xenorhabdus symbionts is barely known. Here, we report a new mechanism of E. coli Nissle (EcN) association with the nematode Steinernema hermaphroditum. We show that EcN cells are enclosed and lysed in at least four pairs of coelomocytes, suggesting these immune cells respond to bacterial invasion. During the IJ stage of nematode development, EcN cells localize to posterior intestinal vacuoles and enter the inter-cuticular space, where they proliferate, aggregate, then lyse. EcN cells expressed proteins in the cell lysates were maintained in the nematode cuticle over eight weeks in non-sterile soil. These observations suggest sequential steps of EcN colonization in the host nematodes involving an immune response that is distinctive from interactions with mutualistic symbiont. Our work establishes a novel framework of nematode-bacteria interaction with potential applications in environmental bioengineering.

microbiology↗

bioRxiv2025

The nematode symbiotic bacterium Xenorhabdus griffiniae can sense and respond to the presence of its host Steinernema hermaphroditum

The mutualistic symbiosis between Xenorhabdus bacteria and Steinernema nematodes has both ecological and practical importance. Their relationship co-evolved to make them dependent on each other in their life cycle where they kill, feed and reproduce within insect larvae together. This behavior has shed light on them as promising candidates to replace conventional pesticides. Despite the importance of the Xenorhabdus in insect-killing, the mechanisms by which the bacteria might sense and respond to the presence of their nematode host are not well understood. We performed an RNA-sequencing experiment on the bacterial partner, X. griffiniae, in close proximity, but not in direct contact with their host nematode, Steinernema hermaphroditum, to identify differentially regulated genes in these conditions, followed by genetic analysis to determine their functional significance. We show that X. griffiniae changes its transcriptomic profile in a small number of genes in the presence of axenic nematodes, but not in the presence of nematodes that are already colonized by X. griffiniae. We select the most differentially regulated gene, ymdA, for further investigation, and show that it plays a role in biofilm formation and affects host colonization efficiency. This work advances our understanding of bacterial sensing of nematodes and motivates future research in deepening our understanding of this underexplored ecological interaction. ImportanceInteractions between different organisms in the soil environment are enabled by the ability to sense and respond to organisms nearby. In many cases, the underlying sensing mechanisms that mediate these ecologically important interactions are not known. Filling in the knowledge gap of how these interactions occur can help us understand how microbial populations organize themselves, establish symbiotic relationships, or compete with other species in complex environments. Furthermore, elucidating these mechanisms may inform the development of new tools in agriculture, such as improved biological control agents. Here we use the bacterial symbiont Xenorhabdus griffiniae of the entomopathogenic nematode Steinernema hermaphroditum to study whether symbiotic bacteria of nematodes are able to sense their presence. Our results suggest that X. griffiniae can sense the presence of its nematode host and respond by modulating the gene expression level of several genes, where at least one, ymdA, has implications for host colonization.

microbiology↗

bioRxiv2025

Parkinson's-Linked Synaptojanin 1 Loss in Dopamine Neurons Triggers Synaptic Degeneration and Striatal TH Interneuron Compensation

Presynaptic endocytic dysfunction is an early feature of Parkinson's disease (PD), but how dopamine circuits adapt to chronic synaptic failure remains unclear. In dopamine neuron-specific Synaptojanin 1 knockout mice, loss of this PD-linked endocytic protein causes terminal dystrophy and striatal dopamine deficiency, yet motor coordination is preserved. Chronic endocytic failure induces striatal dopamine-like neurons (DALNs) with circuit-dependent dopaminergic protein accumulation. DALNs do not arise through transcriptional reprogramming; instead, they acquire dopaminergic proteins from midbrain dopamine neurons through selective long-range transfer that favors soluble cargoes and can convey disease-associated proteins, including -synuclein and tau. Functionally, DALNs support local dopamine production, partially preserve motor performance and increase resistance to acute dopaminergic lesions. This adaptation is shared across PD-linked endocytic mutants and is developmentally constrained, but is not reproduced by acute denervation. Thus, synaptic endocytic stress triggers inter-neuronal protein transfer as an adaptive circuit mechanism supporting dopamine compensation and neuroprotection in early PD.

neuroscience↗

bioRxiv2025

Synaptic changes contribute to persistent extra-motor behaviour deficits in the rNLS8 TDP-43 mouse model of amyotrophic lateral sclerosis

Extra-motor symptoms are increasingly recognised in amyotrophic lateral sclerosis (ALS), encompassing cognitive, social, and behavioural deficits that can substantially impact quality of life. TAR DNA binding protein 43 (TDP-43) pathology is the central disease marker of almost all cases of ALS and approximately half of all frontotemporal dementia (FTD). However, the mechanisms linking TDP-43 pathology with extra-motor symptoms in TDP-43-associated neurodegenerative diseases remain unresolved. In this study, we used the rNLS8 mouse model, which expresses human TDP-43 with an ablated nuclear localisation sequence (hTDP-43∆NLS) in a doxycycline-regulatable manner causing progressive motor decline reminiscent of ALS, to delineate the molecular changes associated with disease-relevant phenotypes. We found that in addition to previously reported dramatic motor decline, rNLS8 mice also develop extra-motor phenotypes consistent with FTD, including disinhibition-like and anxiety-like behaviours, and social interaction impairments. These changes began in the earliest disease stages and remained readily detectable even when rNLS8 mice became severely motor impaired. Notably, extra-motor deficits persisted in rNLS8 mice that had recovered motor function upon hTDP-43∆NLS transgene suppression, regardless of whether recovery was initiated at timepoints prior to or after overt neurodegeneration begins. Transcriptomic analysis of rNLS8 mouse cortex tissues revealed early alterations in expression of 321 genes, most notably involving neuroinflammatory-related pathway activation, and all but 2 of these genes returned to control levels upon suppression of hTDP-43∆NLS expression. Further, 814 genes showed differential exon usage, indicating changes in alternative splicing, in rNLS8 mouse cortex. Of these, differential exon usage of 10 neuronal genes persisted after hTDP-43∆NLS transgene suppression, including synapse component genes Nrxn1, Unc13a, and Gls. Similarly, proteomics analysis of the cortex of rNLS8 mice revealed depletion of synaptic proteins, particularly those involved in glutamatergic signalling pathways, which also persisted following hTDP-43∆NLS transgene suppression. Similar glutamatergic pathway changes were detected in human ALS and FTD post-mortem cortex tissues. Our findings indicate that extra-motor phenotypes emerge early in disease in rNLS8 mice and remain evident despite progressive motor impairments. Further, extra-motor phenotypes persist even upon motor recovery, correlating with specific synaptic gene expression and splicing changes. Overall, this study suggests the potential utility of an expanded suite of behavioural paradigms in preclinical testing using rNLS8 mice, with enhanced relevance to the diversity of TDP-43 proteinopathies including FTD. Our findings further suggest that targeting glutamatergic synaptic components may be an avenue to correct extra-motor deficits associated with TDP-43 pathology.

neuroscience↗

bioRxiv2025

Haplotype rather than single causal variants effects contribute to regulatory gene expression associations in human myeloid cells

Genome-wide association studies typically identify hundreds to thousands of loci, many of which harbor multiple independent peaks, each parsimoniously assumed to be due to the activity of a single causal variant. Fine-mapping of such variants has become a priority and since most associations are located within regulatory regions, it is also assumed that they colocalize with regulatory variants that influence the expression of nearby genes. Here we examine these assumptions by using a moderate throughput expression CROPseq protocol in which Cas9 nuclease is used to induce small insertions and deletions across the credible set of SNPs that may account for expression quantitative trait loci (eQTL) for genes associated with inflammatory bowel disease (IBD). Of the 4,384 SNPs targeted in 88 loci (an average of 50 per locus), 439 were significant and further examined for validation. From these, 98 significantly altered target gene expression in HL-60 myeloid cell line, 74 in induced macrophages from these HL-60 cells, and 78 in induced neutrophils for a total of 201 validated effects (46%), 43 of which were observed in at least two of the cell types. Considering the observed sensitivity and specificity of the controls, we estimate that there are at least 150 true positives per cell type, an average of almost 2.4 for each of the 64 eQTL for which putative causal variants have been fine-mapped. This implies that haplotype effects are likely to explain many of the associations. We also demonstrate that the same approach can be used to investigate the activity of very rare variants in regulatory regions for 89 genes, providing a rapid strategy for establishing clinical relevance of non-coding mutations.

genomics↗

bioRxiv2025

The membrane topology problem inherent in ciliogenesis is solved by ciliary recruitment of a phospholipid flippase

The cilium is a slender cellular projection whose membrane transduces signals essential in development and homeostasis. Although assembly of the axonemal core of the organelle is well-studied, the mechanisms that underlie formation of the [~]250 nm diameter ciliary membrane from oppositely curved 50-100 nm diameter pre-ciliary vesicles remain poorly understood. Here we report that during ciliogenesis in the bi-ciliated alga, Chlamydomonas reinhardtii, aminophospholipid flippase 2 (ALA2) is recruited laterally from a reservoir on the plasma membrane onto the nascent ciliary membrane where it transfers conically shaped phosphatidyl ethanolamine (PE) from the outer to the inner leaflet. In cells lacking ALA2, initiation of cilia regeneration after experimentally induced de-ciliation is delayed, PE flipping is impaired, the ciliary membrane becomes distorted, and cilia that do form are shorter than wild type. Our results uncover a membrane topology problem inherent in ciliogenesis and demonstrate that it is resolved by a phospholipid flippase. HighlightsO_LIMembranes of pre-ciliary vesicles reverse curvature to become the ciliary membrane C_LIO_LIUpon initiation of ciliogenesis, plasma membrane ALA2 transits laterally to cilia C_LIO_LIThe ciliary membranes of ala2 mutants fail to conform to axonemal shape C_LIO_LIALA2 flips PE to establish ciliary membrane curvature C_LI

cell biology↗

bioRxiv2024

Integration of hunger and hormonal state gates infant-directed aggression

Social behaviour is profoundly shaped by internal physiological states. While significant progress has been made in understanding how individual states such as hunger, stress, or arousal modulate behaviour, animals experience multiple states at any given time. The neural mechanisms that integrate such orthogonal states--and how this integration affects behaviour--remain poorly understood. Here we report how hunger and estrous state converge on neurons in the medial preoptic area (MPOA) to shape infant-directed behaviour. We find that hunger promotes pup-directed aggression in normally non-aggressive virgin female mice. This behavioural switch occurs through inhibition of MPOA neurons, driven by the release of neuropeptide Y (NPY) from Agouti-related peptide-expressing neurons in the arcuate nucleus (ArcAgRP neurons). The propensity for hunger-induced aggression is set by reproductive state, with MPOA neurons detecting changes in progesterone (P4) to estradiol (E2) ratio across the estrous cycle. Hunger and estrous state converge on HCN (hyperpolarization-activated cyclic nucleotide-gated) channels, which sets the baseline activity and excitability of MPOA neurons. Using micro-endoscopic imaging, we confirm these findings in vivo, revealing that MPOA neurons encode a state for pup-directed aggression. This work thus provides a mechanistic understanding of how multiple physiological states are integrated to flexibly control social behaviour.

neuroscience↗

bioRxiv2024

Photoactivated SOPP3 enables APEX2-mediated proximity labeling with high spatio-temporal resolution in live cells

Protein interactome characterized via proximity labeling (PL) and proteomic analysis is important for mechanism study in biomedical research. However, exogenous H2O2 required for engineered peroxidase, like APEX2, is cytotoxic, while biotin ligases-based PL have poor temporal resolution. Here, we showed that SOPP3, an engineered photosensitizer, could trigger APEX2 mediated PL within seconds under blue light illumination, without exogenous H2O2 or cytotoxicity. We demonstrated that APEX2 plus photoactivated SOPP3 could catalyze spatially restricted biotinylation at endoplasmic reticulum-mitochondria contact sites and cell-cell interface. Through fusing APEX2 and SOPP3 as a chimeric probe, we showed that APEX2-SOPP3 also works well in multiple subcellular locations, including cell surface. Notably, either APEX2 plus SOPP3, or chimeric APEX2-SOPP3 requires 10 folds lower illumination power, compared to that for light-oxygen-voltage protein alone mediated PL, and has better response to illumination in terms of PL in time course with little cytotoxicity. Thus, this new PL technology paves an avenue to characterize molecular dynamics of key biomedical events with high spatial-temporal resolution, efficiency, and flexible applicability.

molecular biology↗

bioRxiv2024

Stress contingent changes in Hog1 pathway architecture and regulation in Candida albicans

The Hog1 stress-activated protein kinase (SAPK) is a key mediator of stress resistance and virulence in Candida albicans. Hog1 activation via phosphorylation of the canonical TGY motif is mediated by the Pbs2 MAPKK, which itself is activated by the Ssk2 MAPKKK. Although this three-tiered SAPK signalling module is well characterised, it is unclear how Hog1 activation is regulated in response to different stresses. Functioning upstream of the Ssk2 MAPKKK is a two-component related signal transduction system comprising three sensor histidine kinases, a phosphotransfer protein Ypd1, and a response regulator Ssk1. Here, we report that Ssk1 is a master regulator of the Hog1 SAPK that promotes stress resistance and Hog1 phosphorylation in response to diverse stresses, except high osmotic stress. Notably, we find Ssk1 regulates Hog1 in a two-component independent manner by functioning as a scaffolding protein to promote interactions between the Ssk2 and Pbs2 kinases. We propose this scaffolding function is important to maintain a basal level of Hog1 phosphorylation which is necessary for oxidative stress, but not osmotic stress, mediated Hog1 activation. We find that osmotic stress triggers robust Pbs2 phosphorylation which drives its dissociation from Ssk2. In contrast, Pbs2 is not robustly phosphorylated following oxidative stress and the Ssk1-mediated Ssk2-Pbs2 interaction remains intact. Instead, oxidative stress-stimulated increases in phosphorylated Hog1 is dependent on the inhibition of protein tyrosine phosphatases that negatively regulate Hog1 coupled with the Ssk1-mediated promotion of basal Hog1 activity. Furthermore, we find that inhibition of protein tyrosine phosphatases is linked to the hydrogen peroxide induced oxidation of these negative regulators in a mechanism that is dependent thioredoxin. Taken together these data reveal stress contingent changes in Hog1 pathway architecture and regulation and uncover a novel mode of action of the Ssk1 response regulator in SAPK regulation. Author summaryAs a core stress regulator, the Hog1 stress-activated protein kinase (SAPK), is a key virulence determinant in many fungal pathogens. Despite this, little is known regarding the mechanisms by which different stresses trigger the phosphorylation and activation of Hog1. Here we present three novel findings regarding Hog1 regulation in the human fungal pathogen C. albicans. Firstly, we find that the response regulator protein, Ssk1, is a master regulator of Hog1 that forms a scaffold for the upstream Hog1-activating kinases, Ssk2 and Pbs2. Secondly, this scaffolding role maintains a basal level of Hog1 phosphorylation, which is important for responses to stresses, such as oxidative stress, that do not stimulate activation of the upstream Ssk2 and Pbs2 kinases. Instead, oxidative stress induced Hog1 phosphorylation is mediated through the oxidation and inactivation of protein tyrosine phosphatases that negatively regulate Hog1. Finally, we show that high osmotic stress induces the robust phosphorylation and activation of the upstream kinase Pbs2, which drives its dissociation from the Ssk1-mediated scaffold. These new insights into the regulation of the C. albicans Hog1 SAPK pathway offer new strategies to therapeutically target this core virulence determinant.

microbiology↗

bioRxiv2024

Decoding Continuous Character-based Language from Non-invasive Brain Recordings

Deciphering natural language from brain activity through non-invasive devices remains a formidable challenge. Previous non-invasive decoders either require multiple experiments with identical stimuli to pinpoint cortical regions and enhance signal-to-noise ratios in brain activity, or they are limited to discerning basic linguistic elements such as letters and words. We propose a novel approach to decoding continuous language from single-trial non-invasive fMRI recordings, in which a three-dimensional convolutional network augmented with information bottleneck is developed to automatically identify responsive voxels to stimuli, and a character-based decoder is designed for the semantic reconstruction of continuous language characterized by inherent character structures. The resulting decoder can produce intelligible textual sequences that faithfully capture the meaning of perceived speech both within and across subjects, while existing decoders exhibit significantly inferior performance in cross-subject contexts. The ability to decode continuous language from single trials across subjects demonstrates the promising applications of non-invasive language brain-computer interfaces in both healthcare and neuroscience.

neuroscience↗

bioRxiv2024

Analyses of Xenorhabdus griffiniae genomes reveal two distinct sub-species that display intra-species variation due to prophages.

Nematodes of the genus Steinernema and their Xenorhabdus bacterial symbionts are lethal entomopathogens that are useful in the biocontrol of insect pests, as sources of diverse natural products, and as research models for mutualism and parasitism. Xenorhabdus play a central role in all aspects of the Steinernema lifecycle, and a deeper understanding of their genomes therefore has the potential to spur advances in each of these applications. Here, we report a comparative genomics analysis of Xenorhabdus griffiniae, including the symbiont of Steinernema hermaphroditum nematodes, for which genetic and genomic tools are being developed. We sequenced and assembled circularized genomes for three Xenorhabdus strains: HGB2511, ID10 and TH1. We then determined their relationships to other Xenorhabdus and delineated their species via phylogenomic analyses, concluding that HGB2511 and ID10 are Xenorhabdus griffiniae while TH1 is a novel species. These additions to the existing X. griffiniae landscape further allowed for the identification of two subspecies within the clade. Consistent with other Xenorhabdus, the analysed X. griffiniae genomes each encode a wide array of antimicrobials and virulence-related proteins. Comparative genomic analyses, including the creation of a pangenome, revealed that a large amount of the intraspecies variation in X. griffiniae is contained within the mobilome and attributable to prophage loci. In addition, CRISPR arrays, secondary metabolite potential and toxin genes all varied among strains within the X. griffiniae species. Our findings suggest that phage-related genes drive the genomic diversity in closely related Xenorhabdus symbionts, and that these may underlie some of the traits most associated with the lifestyle and survival of entomopathogenic nematodes and their bacteria: virulence and competition. This study establishes a broad knowledge base for further exploration of not only the relationships between X. griffiniae species and their nematode hosts but also the molecular mechanisms that underlie their entomopathogenic lifestyle.

microbiology↗

bioRxiv2024

ChineseEEG: A Chinese Linguistic Corpora EEG Dataset for Semantic Alignment and Neural Decoding

An Electroencephalography (EEG) dataset utilizing rich text stimuli can advance the understanding of how the brain encodes semantic information and contribute to semantic decoding in brain-computer interface (BCI). Addressing the scarcity of EEG datasets featuring Chinese linguistic stimuli, we present the ChineseEEG dataset, a high-density EEG dataset complemented by simultaneous eye-tracking recordings. This dataset was compiled while 10 participants silently read approximately 11 hours of Chinese text from two well-known novels. This dataset provides long-duration EEG recordings, along with pre-processed EEG sensor-level data and semantic embeddings of reading materials extracted by a pre-trained natural language processing (NLP) model. As a pilot EEG dataset derived from natural Chinese linguistic stimuli, ChineseEEG can significantly support research across neuroscience, NLP, and linguistics. It establishes a benchmark dataset for Chinese semantic decoding, aids in the development of BCIs, and facilitates the exploration of alignment between large language models and human cognitive processes. It can also aid research into the brains mechanisms of language processing within the context of the Chinese natural language.

neuroscience↗

bioRxiv2023

Sysrecon: A systematic data-driven tool for genome-scale metabolic reconstructions

Genome-scale metabolic reconstructions contain the information about metabolism, which understands organisms molecular mechanisms better. Different reconstruction procedures are developed to achieve high-quality GSMRs of organisms; however, the descriptions of procedures are vague, meaning that they cannot be qualitatively reproduced, even contradictory, and different published reconstructions may involve different steps. This indicates that there is no unified strategy to quantify the steps in GSMRs. To resolve the problem, we created a R package, Sysrecon, to quantitatively and qualitatively describe the steps of GSMRs in the literature. Sysrecon disassembles GSMR into 93 steps, which are compiled after the comprehensive textual analysis of metabolic reconstructions. Then, Sysrecon decomposes each step of the reconstruction procedure into three components: step content, step conversion, and database and tools. When building a GSMR, Sysrecon creates a template procedure that includes a list of pipeline steps, the description of the information conversion in the steps, and the database and tools that may be used to facilitate the conversion. Because each steps conversion is defined by a formula, the entire GSMR can be dismantled into many step blocks. The reconstruction procedure is therefore transformed into an adaptable automated assembly line that can be customized and tailored to settings of different organisms. To the best of our knowledge, Sysrecon is the first computational tool that dynamically constructs the GSMRs pipeline and provides a framework for defining reconstruction steps and can be used as a basis for the development of high-quality GSMRs.

systems biology↗