Biology subjects

Shi, X.

Publications and source records attributed to Shi, X..

At least 91 records · Page 5Linked to original sources

bioRxiv2024

The consequences of mismatched buffers in spectral cell sorting

Although spectral flow cytometry has become a ubiquitous tool for cell analysis, the use of spectral cytometry on cell sorters requires additional considerations arising from the unique requirements of sorting workflows. Here, we show that care should be taken when ascertaining the purity of a sort on a spectral cell sorter, as the mismatch of buffers used for initial sample suspension and the buffers used for sort collection can affect the unmixing of the data, potentially giving rise to erroneous purity check results.

cell biology↗

bioRxiv2024

Involvement of OsS40-14 in ROS and plastid organization related regulatory networks of dark-induced senescence in rice

Dark-induced senescence triggers significant metabolic changes that recycle resources and ensure plant survival. In this study, we identified a transcription factor OsS40-14 in rice, which can form homo-oligomers. The oss40-14 knockout mutants exhibited stay-green phenotype of primary leaf and flag leaf during dark-induced condition, with substantial retention of chlorophylls and photosynthetic capacity as well as remarkably reduced reactive oxygen species (ROS), while OsS40-14 overexpressing transgenic lines (oeOsS40-14) showed an accelerated senescence phenotype under dark-induced leaf senescence conditions. Transcriptome analysis revealed that when the detached leaves of oss40-14 and WT were treated in darkness condition for 72 hours, 1585 DEGs (|Log2FC| [≥]1, P value<0.05) were reprogrammed in oss40-14 relative to WT. CUT&Tag-seq analysis in protoplast transient expression of OsS40-14 system showed that OsS40-14 was 40.95% enriched in the transcription start site (TSS) of the genome. Sequence clustering analysis showed that OsS40-14 protein was mainly enriched and bound to TACCCACAAGACAC conserved elements. The seed region "ACCCA" of OsS40 proteins was identified by single nucleotide mutagenesis EMSA. The integrative analysis of transcriptome and CUT&Tag-seq datasets showed 153 OsS40-14-targeted DEGs, they mainly enriched in plastid organization and photosynthesis process at dark-induced condition in oss40-14 relative to WT. Among them, eleven candidate targets of OsS40-14 such as Glucose 6-phosphate/phosphate translocator, Na+/H+ antiporter, Catalase, Chitinase 2, Phosphate transporter 19, OsWAK32, and OsRLCK319 were directly targeted and upregulated confirmed by ChIP-PCR and RT-qPCR. It demonstrates a novel model of OsS40-14 mediating macromolecule metabolism and nutrient recycling controls the plastid organization during dark-induced leaf senescence. Significant statementInvolvement of OsS40-14 in macromolecule catabolism, nutrient recycling, and ROS homeostasis revealed a plastid organization defection of dark-induced senescence in rice

plant biology↗

bioRxiv2024

Intra-subgenome regulation induces unbalanced expression and function among bread wheat homoeologs

The differential expression of homoeologous genes confers expression plasticity and facilitates the adaptation and domestication of major polyploid crops. However, how this homoeolog expression bias (HEB) is regulated remains elusive. Here, transcriptome analysis of 406 wheat (Triticum aestivum; AABBDD) accessions revealed great variation in HEB among accessions. We identified 14,727 QTLs regulating HEB (hebQTLs), indicating that HEB is genetically regulated and can be predicted using genotyping data. The hebQTLs only regulate the expression of homoeologs in the same subgenome and downregulate their expression to result in HEB, suggesting that intra-subgenomic rather than inter-subgenomic interactions induce HEB. Furthermore, non-hebQTL-regulated homoeologs have stronger biological functions, are under higher selection pressure and exhibit lower genetic diversity than hebQTL-regulated homoeologs and compensate for the downregulated expressions of hebQTL-regulated homoeologs. Our findings reveal how homoeolog expression is coordinated at the genetic level and provide an avenue for leveraging HEB to improve polyploid crops.

genomics↗

bioRxiv2024

Mapping Genetic Interactions of All Paralogs in the Human Genome

Paralogs are abundant in the human genome and thought to be a primary source of synthetic lethality, yet the vast paralogome remains largely uncharacterized. A digenic screen of all paralogous gene pairs in the human genome revealed that synthetic lethalities were infrequent and varied in penetrance in different tumor backgrounds. We hypothesized that the variable penetrance of synthetic lethalities resulted from complex polygenic interactions with different cellular contexts. A machine learning classifier of a subset of paralog pairs tested across 49 cancer models revealed that endogenous perturbations in related pathways predicted paralog synthetic lethality. Further, predictive modeling of paralog synthetic lethality revealed that the strength of synthetic lethal interactions were largely due to the overlap and essentiality of the protein-protein interaction networks shared by the paralogs pairs. Collectively, this study tested all digenic paralog interactions and delineated the key feature classes that underlie the heterogeneity of paralog synthetic lethalities. HighlightsO_LISynthetic lethal paralogs have long been known, yet most paralog interactions are untested. C_LIO_LIWe report the first combinatorial screen of all 36,648 known human paralog pairs. C_LIO_LIA meta-analysis of 461 paralog pairs in 49 cell models revealed context-dependent interactions. C_LIO_LIThe essentiality of paralog interaction networks dictate the strength of synthetic lethality. C_LI eTOCSynthetic lethal paralogs have long been known, yet most paralog interactions are untested. Flister et al report a screen of all 36,648 known human paralog pairs. These data combined with a meta-analysis of 461 pairs across 49 cell models revealed insights to the molecular underpinnings of context-dependent synthetic lethality. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/603642v3_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@1356ac3org.highwire.dtl.DTLVardef@1f43108org.highwire.dtl.DTLVardef@bf2a26org.highwire.dtl.DTLVardef@6844f8_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Analysis of mixtures of birds and insects in weather radar data

Weather radars are increasingly used to study the spatial-temporal dynamics of airborne birds and insects. These two taxa often co-occur and separating their contributions remains a major analytical challenge. Most studies have restricted analyses to locations, seasons, and periods when one or the other taxa dominates. In this study, we describe an analytical method to estimate the proportion of birds and insects from vertical profiles of biological reflectivities, using a minimal number of assumptions on the airspeeds of birds and insects. We evaluated our method on understudied regions where airborne insect density is too high for existing approaches of studying bird migration with weather radars: the tropics (Colombia) and the southern temperate zone (Southeast Australia). Our method estimates that bird and insect signals routinely reach similar magnitudes in these regions. Retrieved patterns across daily and annual cycles reflected expected biological patterns that are indicative of migratory and non-migratory movements in both climates and migration systems. Compared to fixed airspeed thresholding, we obtain finer separation and retain more spatial-temporal complexity that is crucial to revealing aerial habitat use of both taxa. Our analytical procedure is readily implemented into existing software, empowering ecologists to explore aerial ecosystems outside the northern temperate zone, as well as diurnal migration of birds and insects that remains heavily understudied. Lay summaryO_LIWe developed a new method to differentiate between birds and insects in weather radar data. C_LIO_LIThis method uses minimal assumptions about the flight speeds of birds and insects. C_LIO_LIWe tested the method in regions with high insect density: the tropics (Colombia) and southern temperate zone (Southeast Australia). C_LIO_LIOur method estimated proportions of birds and insects that captured expected patterns of daily and annual movements, which were indicative of migratory and non-migratory movement of both taxa. C_LIO_LIUnlike fixed airspeed criteria for bird and insect separation, our approach provides a more detailed understanding of aerial habitat use by both birds and insects. C_LIO_LIThis method can be easily added to existing software, helping ecologists study bird and insect movements in less-studied areas and ecosystems. C_LI

ecology↗

bioRxiv2024

Histone Tetrasome Dynamics Affects Chromatin Transcription

During various DNA-centered processes in the cell nucleus, the minimal structural units of chromatin organization, nucleosomes, are often transiently converted to hexasomes and tetrasomes missing one or both H2A/H2B histone dimers, respectively. However, the structural and functional properties of the subnucleosomes and their impact on biological processes in the nuclei are poorly understood. Here, using biochemical approaches, molecular dynamics simulations, single-particle Forster resonance energy transfer (spFRET) microscopy and NMR spectroscopy, we have shown that, surprisingly, removal of both dimers from a nucleosome results in much higher mobility of both histones and DNA in the tetrasome. Accordingly, DNase I footprinting shows that DNA-histone interactions in tetrasomes are greatly compromised, resulting in formation of a much lower barrier to transcribing RNA polymerase II than nucleosomes. The data suggest that tetrasomes are remarkably dynamic structures and their formation can strongly affect various biological processes.

molecular biology↗

bioRxiv2024

Rubisco from two ecotypes of Plantago lanceolata L. that are native to sites differing in atmospheric CO2 levels

Rubisco, the most prevalent protein on the planet, initiates the conversion of CO2 into carbohydrates during photosynthesis. Responses of this process to atmospheric CO2 fluctuations daily, seasonally, and over millennia is still poorly understood. We have hypothesized that higher plants maintain carbon-to-nitrogen homeostasis by adjusting the balance of magnesium and manganese in chloroplasts to alter their relative carbon fixation and nitrogen assimilation rates. The following study examined the influence of magnesium and manganese on rubisco carboxylation and oxygenation in protein purified from two ecotypes of Plantago lanceolata: one adapted to the high atmospheric CO2 that occurs near a natural CO2 spring and the other adapted to more typical CO2 atmospheres that occur nearby. The plastid DNA coding for the large unit of rubisco were similar in both ecotypes. The kinetics of rubiscos from the two ecotypes differed more when they were associated with manganese than magnesium. Specificity for CO2 over O2 (Sc/o) for rubiscos from both ecotypes were higher when the enzymes were bound to magnesium than manganese. This disparity may account for the adaptation of this species to different CO2 environments.

plant biology↗

bioRxiv2024

Benchmarking algorithms for spatially variable gene identification in spatial transcriptomics

The rapid development of spatial transcriptomics has underscored the importance of identifying spatially variable genes. As a fundamental task in spatial transcriptomic data analysis, spatially variable gene identification has been extensively studied. However, the lack of comprehensive benchmark makes it difficult to validate the effectiveness of various algorithms scattered across a large number of studies with real-world datasets. In response, this article proposes a benchmark framework to evaluate algorithms for identifying spatially variable genes through the analysis of synthesized and real-world datasets, aiming to identify the best algorithms and their corresponding application scenarios. This framework can assist medical and life scientists in selecting suitable algorithms for their research, while also aid bioinformatics scientists in developing more powerful and efficient computational methods in spatial transcriptomic research.

bioinformatics↗

bioRxiv2024

tauX: A Gene Expression Ratio Strategy to Improve Machine Learning Applications in Precision Medicine

Machine learning algorithms identify patterns that would otherwise be difficult to observe in high-dimensional molecular and clinical data. For this reason, machine learning has the potential to have a profound impact on clinical decision making and drug target discovery. Nevertheless, there remain considerable technical challenges in adapting these tools for clinical use. These challenges include clinical feature engineering, model selection, and defining optimal strategies for model training. For cancer care, RNA sequencing of patient tumor biopsies has already proven to be a powerful molecular assay to characterize tumor-intrinsic and -extrinsic phenotypes influencing therapeutic response. To improve the predictive performance of RNA-sequencing data, we developed the tauX machine learning framework to refine gene expression features and improve the performance of machine learning algorithms. The tauX framework uses aggregated ratios of positively and negatively associated predictive genes to simplify the prediction task. We showed a significant improvement in predictive performance using a large database of synthetic gene expression profiles. We also show how the tauX framework can be used to elucidate the mechanisms of response and resistance to checkpoint blockade therapy using data from the Stand Up to Cancer (SU2C) Lung Response Cohort and The Cancer Genome Atlas (TCGA). The tauX strategy achieved superior predictive performance compared to models built upon established feature engineering strategies or widely used cancer gene expression signatures. The tauX framework is available as a freely deployable docker container (https://hub.docker.com/r/pfeiljx/taux).

bioinformatics↗

bioRxiv2024

Joint exome and metabolome analysis in individuals with dyslexia: Evidence for associated dysregulations of olfactory perception and autoimmune functions

Dyslexia is a learning disability that negatively affects reading, writing, and spelling development at the word level in 5%-9% of children. The phenotype is variable and complex, involving several potential cognitive and physical concomitants such as sensory dysregulation and immunodeficiencies. The biological pathogenesis is not well-understood. Toward a better understanding of the biological drivers of dyslexia, we conducted the first joint exome and metabolome investigation in a pilot sample of 30 participants with dyslexia and 13 controls. In this analysis, eight metabolites of interest emerged (pyridoxine, kynurenic acid, citraconic acid, phosphocreatine, hippuric acid, xylitol, 2-deoxyuridine, and acetylcysteine). A metabolite-metabolite interaction analysis identified Krebs cycle intermediates that may be implicated in the development of dyslexia. Gene ontology analysis based on exome variants resulted in several pathways of interest, including the sensory perception of smell (olfactory) and immune system-related responses. In the joint exome and metabolite analysis, the olfactory transduction pathway emerged as the primary pathway of interest. Although the olfactory transduction and Krebs cycle pathways have not previously been described in dyslexia literature, these pathways have been implicated in other neurodevelopmental disorders including autism spectrum disorder and obsessive-compulsive disorder, suggesting the possibility of these pathways playing a role in dyslexia as well. Immune system response pathways, on the other hand, have been implicated in both dyslexia and other neurodevelopmental disorders.

bioinformatics↗

bioRxiv2024

Exploring Porphyromonas gingivalis Pathogenesis and Antibody Pool Effect Using a Novel Mouse Reproductive Model

This study introduces a novel animal model consisting of two phases. In phase I, Balb/c mice received three intraperitoneal injections of antibodies and two subcutaneous challenges with Porphyromonas gingivalis. The mice were divided into seven groups: G1, G2, and G3 received a single monoclonal antibody targeting the major outer membrane protein RagB of P. gingivalis and infection; G4 was infected without antibody; G5 and G6 received a mixture of monoclonal antibodies and infection; and G7 served as the healthy control. In phase II, one male was paired with one female from the same group and one healthy female. Fertility was assessed using maximum body weight growth rate (MWGR) and alive pup rate (APR). Results indicated that the APR of neonatal mice in G5+G6 significantly lower than G1-G3 and G7 (P < 0.05). Similarly, the MWGR of G5+G6 significantly lower than G7 (P < 0.05). Notably, the APR and MWGR in G4, which received no antibody, were lower than in G7 but higher than in G5-G6. These findings suggest that a mixture of antibodies coexisting with P. gingivalis infection leads to more detrimental reproductive damage than infection alone. The so-called Antibody Pool Effect plays a role in the pathogenesis of P. gingivalis. Understanding the mechanisms of this immunopathological damage may provide insights into the correlation between P. gingivalis infection and systemic diseases.

immunology↗

bioRxiv2024

Coaching ribosome biogenesis from the nuclear periphery

Severe invagination of the nuclear envelope is a hallmark of cancers, aging, neurodegeneration, and infections. However, the outcomes of nuclear invagination remain unclear. This work identified a new function of nuclear invagination: regulating ribosome biogenesis. With expansion microscopy, we observed frequent physical contact between nuclear invaginations and nucleoli. Surprisingly, the higher the invagination curvature, the more ribosomal RNA and pre-ribosomes are made in the contacted nucleolus. By growing cells on nanopillars that generate nuclear invaginations with desired curvatures, we can increase and decrease ribosome biogenesis. Based on this causation, we repressed the ribosome levels in breast cancer and progeria cells by growing cells on low-curvature nanopillars, indicating that overactivated ribosome biogenesis can be rescued by reshaping nuclei. Mechanistically, high-curvature nuclear invaginations reduce heterochromatin and enrich nuclear pore complexes, which promote ribosome biogenesis. We anticipate that our findings will serve as a foundation for further studies on nuclear deformation. HighlightsNuclear invaginations regulate ribosome biogenesis by physically contacting nucleoli. High-curvature nuclear tunnels increase ribosome biogenesis. Nanopillars reduce ribosome biogenesis by transforming high-curvature nuclear invaginations to low-curvature ones.

cell biology↗

bioRxiv2024

Multi-dimensionality of tree communities structure host-parasitoid networks and their phylogenetic composition

Environmental factors can influence ecological networks, but these effects are poorly understood in the realm of the phylogeny of host-parasitoid interactions. Especially, we lack a comprehensive understanding of the ways that biotic factors, including plant species richness, overall community phylogenetic and functional composition of consumers, and abiotic factors such as microclimate, determining host-parasitoid network structure and host-parasitoid community dynamics. To address this, we leveraged a five-year dataset of trap-nesting bees and wasps and their parasitoids collected in a highly-controlled, large-scale subtropical tree biodiversity experiment. We tested for effects of tree species richness, tree phylogenetic and functional diversity, and species and phylogenetic composition on species and phylogenetic diversity of both host and parasitoid communities and the composition of their interaction networks. We show that multiple components of tree diversity and canopy cover impacted both, species and phylogenetic composition of hosts and parasitoids. Generally, phylogenetic associations between hosts and parasitoids reflected non-randomly structured interactions between phylogenetic trees of hosts and parasitoids. Further, host-parasitoid network structure was influenced by tree species richness, tree phylogenetic diversity, and canopy cover. Our study indicates that the composition of higher trophic levels and corresponding interaction networks are determined by plant diversity and canopy cover especially via trophic links in species-rich ecosystems.

ecology↗

bioRxiv2024

Reducing competition between msd and genomic DNA significantly improved the editing efficiency of the retron editing system

A retron is a distinct system encoding reverse transcriptase and a unique single-stranded DNA/RNA hybrid called multicopy single-stranded DNA (msDNA). The ability of msDNA to serve as a homologous recombination donor for gene editing has attracted great interest. However, the mechanism by which msDNA expression affects editing efficiency remains unclear. In this study, we show that an increase in msd number increased msDNA yield but was not necessarily accompanied by an increase in editing efficiency. Mechanistic studies indicate that msd and genomic regions competed for msDNA during recombination. As the number of msd increased, the amount of msDNA allocated to the genomic targets decreased, resulting in a decrease in editing efficiency. Finally, we reduced msd editing by expressing msDNA corresponding to the plasmid replication leading strand sequence, thus constructing a retron-based gene editing system that achieved 100% editing efficiency in the shortest time reported to date. The above results reveal a completely different features between retron-based gene editing system and oligonucleotide-mediated gene editing system and will provide theoretical guidance for the design and application of the retron system.

synthetic biology↗

bioRxiv2024

Pandemic Vibrio parahaemolyticus wave succession by gene loss

While spontaneous mutation and gene acquisition are well-established drivers of pathogen adaptation, the role of gene loss remains underexplored. Here, we investigated the emergence and diversification of the pandemic clone (PC) of Vibrio parahaemolyticus through large-scale phylogenomic analysis of 8,684 global isolates. The PC rapidly acquired multiple marker genes and genomic islands, subsequently diverging into successive sublineages mediating independent waves of cross-country transmission, as also observed in V. cholerae. Wave succession in the last two decades was driven by loss of putrescine utilization (Puu) genes, conferring phenotypic advantages for environmental adaptation (enhanced biofilm formation) and human transmission (increased cell adhesion/intestinal colonization, reduced virulence), consistent with the virulence trade-off hypothesis. We identified Puu-gene loss in multiple bacterial genera, with effects on biofilm and adhesion replicated in V. cholerae and Escherichia coli, suggesting convergent evolution and universal phenotypic effects. Our results highlight the indispensable role of gene loss in bacterial pathogen adaptation.

microbiology↗

bioRxiv2024

The 11β-hydroxysteroid dehydrogenase type 1 inhibitor SPI-62 prevents morbidity in a mouse model of Cushing's syndrome

11{beta}-hydroxysteroid dehydrogenase type 1 (HSD-1) inhibitors represent a potential therapeutic approach for patients with Cushings syndrome, autonomous cortisol secretion (ACS), or iatrogenic glucocorticoid (GC) excess. We assessed whether the HSD-1 inhibitor SPI-62 prevents GC-associated morbidity in a mouse Cushings syndrome model. Corticosterone (CORT) was administered to mice for 5 weeks. Animals who received CORT were randomized between vehicle and 3 SPI-62 regimens. A control group received neither CORT nor SPI-62. Body weight was measured daily to enable weight-based SPI-62 administration. Food consumption by pair-housed animals was reported weekly. Insulin sensitivity was evaluated by fasting homeostatic model assessment of insulin resistance. Adiposity and skeletal myopathy were measured using magnetic resonance imaging and post-mortem weights of fat depots and skeletal muscles. Grip strength was measured with a digital meter. Ambulation behavior in an open field maze was assessed. Post-mortem dermal thickness was quantified. Skin structure was evaluated by histology. CORT was associated with decreased insulin sensitivity, increased adiposity, skeletal myoatrophy, reduced grip strength, decreased dermal thickness, and skin structural changes. A trend of increased food consumption and an unexpected biphasic weight change were observed with CORT. SPI-62 attenuated all observed adverse effects in a dose-dependent manner. In general, results for the high SPI-62 regimen were similar as those in animals who received no CORT, suggesting that full HSD-1 inhibition should be maintained throughout a dose interval to mitigate the effects of glucocorticoid excess.

pharmacology and toxicology↗

bioRxiv2024

Genome sequencing of 'Fuji' apple clonal varieties reveals evolutionary history and genetic mechanism of the spur-type morphology

Somatic variations arising during asexual reproduction can lead to the emergence of bud sports exhibiting advantageous traits, forming the basis for bud sport breeding in perennial plants. Here, we report a near-complete, fully phased genome assembly of Fuji apple, enabling comprehensive identification of somatic variants across 74 clonally propagated Fuji varieties. Phylogenetic analysis of Fuji sport varieties indicates that the emergence of spur-type and early maturation traits results from multiple independent formation events. A number of putative functional somatic variants are identified, including one spur-type specific deletion located in the promoter of the TCP transcription factor gene MdTCP11. DNA methylation level of the deletion-associated miniature inverted-repeat transposable element is lower in the spur-type varieties compared to the standard-type varieties, while the expression of MdTCP11 is significantly higher. Overexpression of MdTCP11 in apple decreases the plant height, highlighting its important role in the development of spur-type apple varieties. This study sheds light on the 80-year cloning history of Fuji and provides valuable candidate causative mutations for apple breeding.

plant biology↗

bioRxiv2024

A metabolic atlas of mouse aging

Humans are living longer, but this is accompanied by an increased incidence of age-related chronic diseases. Many of these diseases are influenced by age-associated metabolic dysregulation, but how metabolism changes in multiple organs during aging in males and females is not known. Answering this could reveal new mechanisms of aging and age-targeted therapeutics. In this study, we describe how metabolism changes in 12 organs in male and female mice at 5 different ages. Organs show distinct patterns of metabolic aging that are affected by sex differently. Hydroxyproline shows the most consistent change across the dataset, decreasing with age in 11 out of 12 organs investigated. We also developed a metabolic aging clock that predicts biological age and identified alpha-ketoglutarate, previously shown to extend lifespan in mice, as a key predictor of age. Our results reveal fundamental insights into the aging process and identify new therapeutic targets to maintain organ health.

molecular biology↗