Biology subjects

Yang, C.

Publications and source records attributed to Yang, C..

At least 199 records · Page 11Linked to original sources

bioRxiv2024

GCI: a continuity inspector for complete genome assembly

MotivationRecent advances in long-read sequencing technologies have significantly facilitated the production of high-quality genome assembly. The telomere-to-telomere (T2T) gapless assembly has become the new golden standard of genome assembly efforts. Several recent efforts have claimed to produce T2T level reference genomes. However, a universal standard is still missing to qualify a genome assembly to be at T2T standard. Traditional genome assembly assessment metrics (N50 and its derivatives) have no capacity in differentiate between nearly T2T assembly and the truly T2T assembly in continuity either globally and locally. Also these metrics are independent of raw reads, which make them inflated easily by artificial operations. Therefore a gaplessness evaluation tool at single nucleotide resolution to reflect true completeness is urgently needed in the era of complete genomes. ResultsHere, we present a tool called Genome Continuity Inspector (GCI) to assess genome assembly continuity at the single base resolution, that can evaluate how close a genome assembly is close to T2T level. GCI utilized multiple aligners to map long reads from multiple platforms back to the assembly. By incorporating curated mapping coverage of high-confidence read alignments, GCI identifies potential assembly issues. Meanwhile, it also reports GCI scores to quantify the assembly overall continuity in the whole genome or chromosome scale. Availability and implementationThe open-source GCI code is freely available on Github (https://github.com/yeeus/GCI) under the MIT license.

bioinformatics↗

bioRxiv2024

Comparative genomics of macaques and integrated insights into genetic variation and population history

The crab-eating macaques (Macaca fascicularis) and rhesus macaques (M. mulatta) are widely studied nonhuman primates in biomedical and evolutionary research. Despite their significance, the current understanding of the complex genomic structure in macaques and the differences between species requires substantial improvement. Here, we present a complete genome assembly of a crab-eating macaque and 20 haplotype-resolved macaque assemblies to investigate the complex regions and major genomic differences between species. Segmental duplication in macaques is [~]42% lower, while centromeres are [~]3.7 times longer than those in humans. The characterization of [~]2 Mbp fixed genetic variants and [~]240 Mbp complex loci highlights potential associations with metabolic differences between the two macaque species (e.g., CYP2C76 and EHBP1L1). Additionally, hundreds of alternative splicing differences show post-transcriptional regulation divergence between these two species (e.g., PNPO). We also characterize 91 large-scale genomic differences between macaques and humans at a single-base-pair resolution and highlight their impact on gene regulation in primate evolution (e.g., FOLH1 and PIEZO2). Finally, population genetics recapitulates macaque speciation and selective sweeps, highlighting potential genetic basis of reproduction and tail phenotype differences (e.g., STAB1, SEMA3F, and HOXD13). In summary, the integrated analysis of genetic variation and population genetics in macaques greatly enhances our comprehension of lineage-specific phenotypes, adaptation, and primate evolution, thereby improving their biomedical applications in human diseases.

genomics↗

bioRxiv2024

Myosin A and F-Actin play a critical role in mitochondrial dynamics and inheritance in Toxoplasma gondii

The single mitochondrion of the obligate intracellular parasite Toxoplasma gondii is highly dynamic. Toxoplasmas mitochondrion changes morphology as the parasite moves from the intracellular to the extracellular environment and during division. Toxoplasmas mitochondrial dynamic is dependent on an outer mitochondrion membrane-associated protein LMF1 and its interaction with IMC10, a protein localized at the inner membrane complex (IMC). In the absence of either LMF1 or IMC10, parasites have defective mitochondrial morphology and inheritance defects. As little is known about mitochondrial inheritance in Toxoplasma, we have used the LMF1/IMC10 tethering complex as an entry point to dissect the machinery behind this process. Using a yeast two-hybrid screen, we previously identified Myosin A (MyoA) as a putative interactor of LMF1. Although MyoA is known to be located at the parasites pellicle, we now show through ultrastructure expansion microscopy (U-ExM) that this protein accumulates around the mitochondrion in the late stages of parasite division. Parasites lacking MyoA show defective mitochondrial morphology and a delay in mitochondrion delivery to the daughter parasite buds during division, indicating that this protein is involved in organellar inheritance. Disruption of the parasites actin network also affects mitochondrion morphology. We also show that parasite-extracted mitochondrion vesicles interact with actin filaments. Interestingly, mitochondrion vesicles extracted out of parasites lacking LMF1 pulled down less actin, showing that LMF1 might be important for mitochondrion and actin interaction. Accordingly, we are showing for the first time that actin and Myosin A are important for Toxoplasma mitochondrial morphology and inheritance.

microbiology↗

bioRxiv2024

Non-invasive laser speckle imaging of extra-embryonic blood vessels in intact few-days-old avian eggs

Imaging blood vessels in early-stage avian embryos has a wide range of practical applications for developmental biology studies, drug and vaccine testing, and early sex determination. Optical imaging such as brightfield transmission imaging offers a compelling solution due to its safe non-ionizing radiation, and operational benefits. However, it comes with challenges such as eggshell opacity and light scattering. To address these, we have revisited an approach based on laser speckle contrast imaging (LSCI) and demonstrated a high quality, comprehensive and non-invasive visualization of blood vessels in few-days-old chicken eggs, with blood vessel as small as 100 {micro}m in diameter (with LSCI profile full-width-at-half-maximum of 275 {micro}m). We present its non-invasive use for monitoring blood flow, measuring the embryos heartbeat, and determining the embryos developmental stages using machine learning with 85% accuracy from stage HH15 to HH22. This method can potentially be used for non-invasive longitudinal studies of cardiovascular development and angiogenesis, as well as egg screening for the poultry industry.

bioengineering↗

bioRxiv2024

Design and optimization of novel succinate dehydrogenase inhibitors against agricultural fungi based on Transformer model

Succinate dehydrogenase inhibitors (SDHIs) are a promising class of fungicides targeting the energy production pathway of pathogenic fungi. However, overuse has led to resistance, necessitating the development of new and effective SDHIs. This study takes the Transformer model to generate a customized virtual library of potential SDHIs. These candidates were then meticulously screened based on expert knowledge and synthetic feasibility, ultimately yielding several pyrazole carboxamide derivatives as the promising leads. Subsequent synthesis, antifungal activity testing, and structural optimization further refined these leads into potent SDHI candidates. This work marks the first application of a generative model to SDHI design, establishing a robust workflow for virtual library generation, screening, activity evaluation, and structure optimization. This provides one way for the rational design of future SDHIs, not only against fungi, but potentially other agricultural pathogens as well.

biochemistry↗

bioRxiv2024

High-precision photoacoustic neural modulation uses a non-thermal mechanism

Neuromodulation is a powerful tool for fundamental studies in neuroscience and potential treatments of neurological disorders. Both photoacoustic (PA) and photothermal (PT) effects have been harnessed for non-genetic high-precision neural stimulation. Using a fiber-based device excitable by a nanosecond pulsed laser and a continuous wave laser for PA and PT stimulation, respectively, we systematically investigated PA and PT neuromodulation at single neuron level. Our results show that the laser energy needed for PA neurostimulaion is 1/40 of that needed for PT stimulation to achieve the same level of cell response recorded by Ca2+ imaging. The threshold energy for PA stimulation is found to be further reduced in neurons overexpressing mechano-sensitive channels, indicating the direct involvement of mechano-sensitive channels in PA stimulation. Electrophysiology study of single neurons upon PA and PT stimulation was performed by patch clamp recordings. Electrophysiological features stimulated by PA are distinct from those induced by PT, confirming that PA and PT stimulations operate through distinct mechanisms. These insights offer a foundation for rational design of more efficient and safer non-genetic neural modulation approaches.

neuroscience↗

bioRxiv2024

Investigating 3D microbial community dynamics in the rhizosphere using complex-field and fluorescence microscopy

Microbial interactions in the rhizosphere contribute to soil health. Understanding these interactions thus has the potential to advance sustainable agriculture, ecosystem management, and environmental stewardship. Yet it is difficult to understand what we cannot see; amongst the limitations in rhizosphere imaging are challenges associated with rapidly and non-invasively imaging microbial cells over field depths relevant to plant roots. Here, we present a novel bimodal imaging technique called Complex-field and Fluorescence microscopy using the Aperture Scanning Technique (CFAST) that begins to address these limitations by integrating quantitative phase and 3D fluorescence imaging. We showcase CFASTs practicality and versatility in two ways. First, by harnessing its depth of field of more than 100 microns, we significantly reduce the number of captures required for 3D imaging of plant roots and bacteria in the rhizoplane, thereby minimizing potential photobleaching and phototoxicity. Second, by leveraging CFASTs phase sensitivity and fluorescence specificity, we track early bacterial aggregate development, bacterial competition, and gene expression under varying environmental conditions. Specifically, we resolve bacterial growth dynamics of mixed populations at the early stages of colonization without the need for genetically labeling environmental isolates. Moreover, we find that the expression of genes of interest to rhizosphere chemistry (e.g. representative genes involved in phosphorus-sensing and antibiotic production) varies spatiotemporally within microbial populations that are surface-attached and appears distinct from their expression in planktonic cultures. Together, CFASTs attributes overcome commercial imaging platform limitations and enable new insights to be gained into microbial behavioral dynamics in experimental systems of relevance to the rhizosphere.

microbiology↗

bioRxiv2024

Functional architecture of intracellular oscillations in hippocampal dendrites

Fast electrical signaling in dendrites is central to neural computations that support adaptive behaviors. Conventional techniques lack temporal and spatial resolution and the ability to track underlying membrane potential dynamics present across the complex three-dimensional dendritic arbor in vivo. Here, we perform fast two-photon imaging of dendritic and somatic membrane potential dynamics in single pyramidal cells in the CA1 region of the mouse hippocampus during awake behavior. We study the dynamics of subthreshold membrane potential and suprathreshold dendritic events throughout the dendritic arbor in vivo by combining voltage imaging with simultaneous local field potential recording, post hoc morphological reconstruction, and a spatial navigation task. We systematically quantify the modulation of local event rates by locomotion in distinct dendritic regions and report an advancing gradient of dendritic theta phase along the basal-tuft axis, then describe a pre-dominant hyperpolarization of the dendritic arbor during sharp-wave ripples. Finally, we find spatial tuning of dendritic representations dynamically reorganizes following place field formation. Our data reveal how the organization of electrical signaling in dendrites maps onto the anatomy of the dendritic tree across behavior, oscillatory network, and functional cell states.

neuroscience↗

bioRxiv2024

Enhancing Plant Photosynthesis using Carbon Dots as Light Converter and Photosensitizer

Improving photosynthetic efficiency is pivotal for CO2-based biomanufacturing and agriculture purposes. Despite the progress on photosynthetic biohybrids integrating biocatalysts with synthetic materials, nanomaterials with improved optical and photoelectrochemical properties are still needed to increase the energy-conversion efficiency. Here, we present a novel approach using carbon dots (CDs) as both intracellular photosensitizers and light converters for enhancing solar energy utilization in photosynthetic organisms. The CDs were produced from cyanobacterial biomass and used to convert a broad spectrum of solar irradiation to red light. We demonstrated that the nanosized CDs were incorporated into cyanobacterial cells and transferred light-excited electrons into the photosynthetic electron transfer chain. The biohybrids consisting of the CDs and Synechococcus elongatus exhibited increased growth rates, enhanced activities of both photosystems, and accelerated linear electron transport, compared with the cyanobacterial cells only. The supplementation of the CDs increased CO2-fixation rate and CO2-to-glycerol production by 2.4-fold and 2.2-fold, respectively. Furthermore, the CDs were shown to enhance photosynthesis and promote growth of Arabidopsis thaliana. The fresh weight of plant was increased 1.8-fold by CDs addition. These results reveal that simultaneous photosensitization and spectral modification could substantially improve the efficiency of natural photosynthesis. This study presents CDs as an attractive nanomaterial with great application potential in agriculture and solar-powered biomanufacturing.

synthetic biology↗

bioRxiv2024

Large-scale multi-omics analyses identified root-microbiome associations underlying plant nitrogen nutrition

The microbiome determines the performance and fitness of the host plant. Nevertheless, the causal interaction between host genetic variation, gene regulation and the impact of the microbiome on the host phenotype remain unknown. Here we generated 1,341 paired root transcriptome, rhizosphere microbiome and root ionome samples and performed a multi-omics analyses of the host-microbe association at the root-soil interface using 175 rapeseeds (Brassica napus L.) resequenced ecotypes at two field environments. We observed the highest statistically explained variance for root nitrogen uptake among natural ionomic variation by overall transcriptome-wide gene expression and microbial abundance variation. Moreover, we identified significant genome-wide associations for 203 highly heritable amplicon sequence variants (ASVs) at multiple genetic loci regulated by eQTL hotspots associated with nitrogen metabolism components. These associations involved a central bacterial genus (Sphingopyxis), which plays a dominant role on gene regulatory effect on its variation regulated by eQTL hotspots. In addition, we performed high-throughput bacterial cultivation from rapeseed roots and subjected Sphingopyxis to whole genome sequencing. Finally, targeted metabolite profiling and confocal imaging assays demonstrated a host-microbiome regulatory effect on Sphingopyxis established by lateral root development and plant nitrogen nutrition. In summary, our integrative approach reveals the genetic basis of host-microbiome trait associations in the transcriptional, nutritional and environmental domains and suggests that the microbiome might have causal effects on root development with implications towards the breeding of nutrient-efficient crops.

plant biology↗

bioRxiv2024

KR158 spheres harboring slow-cycling cells recapitulate GBM features in an immunocompetent system

Glioblastoma (GBM) poses a significant challenge in clinical oncology due to its aggressive nature, heterogeneity, and resistance to therapies. Cancer stem cells (CSCs) play a critical role in GBM, particularly in treatment-resistance and tumor relapse, emphasizing the need to comprehend the mechanisms regulating these cells. Also, their multifaceted contributions to the tumor-microenvironment (TME) underline their significance, driven by their unique properties. This study aimed to characterize glioblastoma stem cells (GSCs), specifically slow-cycling cells (SCCs), in an immunocompetent murine GBM model to explore their similarities with their human counterparts. Using the KR158 mouse model, we confirmed that SCCs isolated from this model exhibited key traits and functional properties akin to human SCCs. KR158 murine SCCs, expanded in the gliomasphere assay, demonstrated sphere forming ability, self-renewing capacity, positive tumorigenicity, enhanced stemness and resistance to chemotherapy. Together, our findings validate the KR158 murine model as a framework to investigate GSCs and SCCs in GBM-pathology, and explore specifically the SCC-immune system communications, understand their role in disease progression, and evaluate the effect of therapeutic strategies targeting these specific connections.

cancer biology↗

bioRxiv2024

Engineered minimal type I CRISPR-Cas system for transcriptional activation and base editing in human cells

Type I CRISPR-Cas systems are widespread and have exhibited remarkable versatility and efficiency in genome editing and gene regulation in prokaryotes. However, due to the multi-subunit composition and large size, their application in eukaryotes has not been thoroughly investigated. Here, we demonstrate that the type I-F2 Cascade, the most compact among type I systems and significantly smaller than SpCas9, can be developed into programmable tools for use in human cells. For transcriptional activation, the efficiency of the tool based on the engineered I-F2 system can match or surpass that of dCas9. Besides, narrow editing windows limit the application of base editors. Although the R-loop formed by Cascade is much wider than that by Cas9 or Cas12, the potential of base editing with Cascade has not yet been explored. We successfully created a base editor with the I-F2 Cascade, which induces a considerably wide editing window ([~]30 nt) with a bimodal distribution. The wide editing window can expand the range of targetable sites and can be useful for disrupting functional sequences and genetic screening. The editing efficiency can achieve 50% in human cells. This research underscores the application potential of compact type I systems in eukaryotes and developed a new base editor with an extraordinary wide editing window.

molecular biology↗

bioRxiv2024

Δ9-tetrahydrocannabinol (THC) Increases the Rewarding Value of Oxycodone During Self-Administration in Rats

BackgroundCannabis may reduce the nonmedical use of prescription opioids. Causality of polydrug use is difficult to establish from epidemiological data, and thus controlled laboratory models can test whether cannabinoid co-use with opioids can modulate opioid intake. MethodsMale and female rats were trained to intravenously self-administer (IVSA) oxycodone (0.15 mg/kg/infusion) during 6 h sessions. Separate groups were injected with the vehicle or with THC (5 mg/kg, i.p.; N=10) 30 minutes before sessions for the first three weeks. Treatments were swapped in the fourth week. One male group was trained in the intracranial self-stimulation (ICSS) procedure and assessed for brain reward thresholds prior to each IVSA session. ResultsTHC treated animals self-administered less oxycodone during acquisition, with a larger differential expressed in the female group. Tolerance to the THC effect developed over the initial weeks, and increasing the dose of THC (10 mg/kg, i.p.) prolonged the suppressing effect on IVSA. While ICSS thresholds increased with sequential IVSA sessions, no differences between THC- and Vehicle-treated groups were observed. Oxycodone IVSA was increased following the first 60 h abstinence interval in THC-treated, but not vehicle-treated, rats. Acute injection of THC, when all animals had been THC abstinent for several weeks, increased breakpoints in a Progressive Ratio procedure. ConclusionThese data support the interpretation that THC enhances the reinforcing efficacy of a given dose of oxycodone and may therefore increase the addiction liability.

neuroscience↗

bioRxiv2024

Chromosome-scale genome assembly of bread wheat's wild relative Triticum timopheevii

Wheat (Triticum aestivum) is one of the most important food crops with an urgent need for increase in its production to feed the growing world. Triticum timopheevii (2n = 4x = 28) is an allotetraploid wheat wild relative species containing the At and G genomes that has been exploited in many pre-breeding programmes for wheat improvement. In this study, we report the generation of a chromosome-scale reference genome assembly of T. timopheevii accession PI 94760 based on PacBio HiFi reads and chromosome conformation capture (Hi-C). The assembly comprised a total size of 9.35 Gb, featuring a contig N50 of 42.4 Mb, and 166,325 predicted gene models. DNA methylation analysis showed that the G genome had on average more methylated bases than the At genome. The G genome was also more closely related to the S genome of Aegilops speltoides than to the B genome of hexaploid or tetraploid wheat. In summary, the T. timopheevii genome assembly provides a valuable resource for genome-informed discovery of agronomically important genes for food security.

plant biology↗

bioRxiv2024

Automating the Human Connectome Project's Temporal ICA Pipeline

Functional magnetic resonance imaging (fMRI) data are dominated by noise and artifacts, with only a small fraction of the variance relating to neural activity. Temporal independent component analysis (tICA) is a recently developed method that enables selective denoising of fMRI artifacts related to physiology such as respiration. However, an automated and easy to use pipeline for tICA has not previously been available; instead, two manual steps have been necessary: 1) setting the group spatial ICA dimensionality after MELODICs Incremental Group-PCA (MIGP) and 2) labeling tICA components as artifacts versus signals. Moreover, guidance has been lacking as to how many subjects and timepoints are needed to adequately re-estimate the temporal ICA decomposition and what alternatives are available for smaller groups or even individual subjects. Here, we introduce a nine-step fully automated tICA pipeline which removes global artifacts from fMRI dense timeseries after sICA+FIX cleaning and MSMAll alignment driven by functionally relevant areal features. Additionally, we have developed an automated "reclean" Pipeline for improved spatial ICA (sICA) artifact removal. Two major automated components of the pipeline are 1) an automatic group spatial ICA (sICA) dimensionality selection for MIGP data enabled by fitting multiple Wishart distributions; 2) a hierarchical classifier to distinguish group tICA signal components from artifactual components, equipped with a combination of handcrafted features from domain expert knowledge and latent features obtained via self-supervised learning on spatial maps. We demonstrate that the dimensionality estimated for the MIGP data from HCP Young Adult 3T and 7T datasets is comparable to previous manual tICA estimates, and that the group sICA decomposition is highly reproducible. We also show that the tICA classifier achieved over 0.98 Precision-Recall Area Under Curve (PR-AUC) and that the correctly classified components account for over 95% of the tICA-represented variance on multiple held-out evaluation datasets including the HCP-Young Adult, HCP-Aging and HCP-Development datasets under various settings. Our automated tICA pipeline is now available as part of the HCP pipelines, providing a powerful and user-friendly tool for the neuroimaging community.

neuroscience↗

bioRxiv2024

A Novel Imaging Mass Spectrometry Computational Tool for Biomedical Discovery: Untargeted pixel-by-pixel imaging of Metabolite Ratio Pairs

Mass spectrometry imaging (MSI) is a powerful technology used to define the spatial distribution and relative abundance of metabolites across tissue cryosections. While software packages exist for pixel-by-pixel individual metabolite and limited target pairs of ratio imaging, the research community lacks an easy computing and application tool that images any metabolite abundance ratio pairs. Importantly, recognition of correlated metabolite pairs may contribute to the discovery of unanticipated molecules in shared metabolic pathways. Here, we describe the development and implementation of an untargeted R package workflow for pixel-by-pixel ratio imaging of all metabolites detected in an MSI experiment. Considering untargeted MSI studies of murine brain and embryogenesis, we demonstrate that ratio imaging minimizes systematic data variation introduced by sample handling, markedly enhances spatial image contrast, and reveals previously unrecognized metabotype-distinct tissue regions. Furthermore, ratio imaging facilitates identification of novel regional biomarkers and provides anatomical information regarding spatial distribution of metabolite-linked biochemical pathways. The algorithm described herein is applicable to any MSI dataset containing spatial information for metabolites, peptides or proteins, offering a potent hypothesis generation tool to enhance knowledge obtained from current spatial metabolite profiling technologies.

bioinformatics↗

bioRxiv2024

A mouse model to study glutathione limitation in vivo

Glutathione (GSH) is a highly abundant tripeptide thiol that performs diverse protective and biosynthetic functions in cells. While changes in GSH availability are linked to many diseases, including cancer and neurodegenerative disorders, determining the function of GSH in physiology and disease has been challenging due to its tight regulation. To address this, we generated cell and mouse models that express a bifunctional glutathione-synthesizing enzyme from Streptococcus Thermophilus (GshF). GshF expression allows efficient production of GSH in the cytosol and mitochondria and prevents cell death in response to GSH depletion, but not ferroptosis, indicating that GSH is not a limiting factor under lipid peroxidation. CRISPR screens using engineered enzymes revealed metabolic liabilities under compartmentalized GSH depletion. Finally, GshF expression in mice is embryonically lethal but sustains postnatal viability when restricted to adulthood. Overall, our work identifies a conditional mouse model to investigate the role of GSH availability in physiology and disease.

genetics↗

bioRxiv2024

ASY3 has dosage-dependent diverse effects on meiotic crossover formation

Crossovers create genetic diversity and are required for equal chromosome segregation during meiosis. Their number and distribution are highly regulated by different, yet not fully understood mechanisms including crossover interference. Crucial for crossover formation is the chromosome axis. Here, we explore the function of the axis protein ASY3. To this end, we use the allotetraploid species Brassica napus and due to its polyploid nature, this system allows a fine-grained dissection of the dosage of meiotic regulators. The simultaneous mutation of all four ASY3 alleles results in defective synapsis and drastic reduction of crossovers, which is largely rescued by the presence of only one functional ASY3 allele. Crucially, while the number of class I crossovers in mutants with two functional ASY3 alleles is comparable to that in wildtype, this number is significantly increased in mutants with only one functional ASY3 allele, indicating that reducing the dosage of ASY3 increases crossover formation. Moreover, the class I crossovers on each bivalent in mutants with one functional ASY3 allele follow a random distribution, indicating compromised crossover interference. These results reveal the dosage-dependent distinct effects of ASY3 on crossover formation, and provide insights into the role of chromosome axis in patterning recombination.

plant biology↗