Biology subjects

Xu, K.

Publications and source records attributed to Xu, K..

At least 163 records · Page 9Linked to original sources

bioRxiv2023

Evolutionary rescue under demographic and environmental stochasticity

Wild populations suffer two types of stochasticity: demographic stochasticity, from sampling error in offspring number, and environmental stochasticity, from temporal variation of the growth rate. By modeling evolution through phenotypic selection following an abrupt environmental change, we investigate how genetic and demographic dynamics, as well as effects of selection intensity after the environmental change and genetic variance on population survival, differ under demographic and environmental stochasticity. We find that the survival probability declines sharply with stronger selection under demographic stochasticity, but declines more continuously under environmental stochasticity. However, the genetic variance that confers the highest survival probability differs little under demographic and environmental stochasticity. Since the influence of demographic stochasticity is stronger when population size is smaller, a slow initial decline of genetic variance which allows quicker evolution and increase of fitness, is important for persistence. In contrast, the influence of environmental stochasticity is density-independent, so higher initial fitness becomes important for survival under strong environmental stochasticity. Combining both types of stochasticity shows that adding even weak environmental stochasticity can exaggerate the effects of different levels of demographic stochasticity on survival probabilities. Our work suggests the importance of explicitly distinguishing and measuring the forms of stochasticity for evolutionary rescue studies.

evolutionary biology↗

bioRxiv2023

Evolution of pollination-induced plasticity of flower longevity

In many plants, pollen deposition or removal can lead to early flower senescence, while flowers will live longer when pollination is excluded, and the strength of this pollination-induced plasticity of flower longevity varies across populations. This study builds models to investigate the evolution of the plasticity of flower longevity through group and individual selection under stochastic pollination environments. Generally, stronger plasticity evolves when female and male fitness accrual rates are higher and more volatile, and the evolution of plasticity is also strongly affected by daily maintenance cost of flowers relative to construction costs. Group selection only selects for plasticity in the female function (i.e., ovule fertilization) but not in the male function (i.e., pollen removal), and plasticity is optimal in maximizing fitness only when saved resources through plasticity greatly enhance individual fitness. Plasticity is more likely to evolve under individual selection, but under the same pollination environment, any combination of the plasticity in female and male functions that adds up to a certain overall strength of plasticity can be evolutionarily stable. Given the fact that plasticity in the male function is rare in hermaphroditic populations, the plasticity of flower longevity may evolve mainly through group selection instead of individual selection.

evolutionary biology↗

bioRxiv2023

Effects of selfing on the evolution of sexual and asexual reproduction

Plants exhibit diverse breeding systems, with populations capable of outcrossing, selfing, and/or asexual reproduction. However, interactions between the three reproductive pathways remain not fully clear. Sexual reproduction introduces segregation and recombination, but incurs several costs. Selfing can affect the relative costs and benefits of sexual vs. asexual reproduction. Building population genetic models, I explore how selfing affects the evolution of a sexual reproduction rate modifier via (1) indirect selection due to segregation, (2) indirect selection from changes in recombination rates, and (3) selection from the cost of meiosis and mate limitation. The dominant selective force mediating the evolution of sex is found to vary with the rate of sexual reproduction and selfing, but selective force (1) and (3) are generally stronger than selective force (2). A modifier enhancing sexual reproduction tends to be favored by indirect selection generated by partially recessive, small-effect deleterious mutations, while hindered by highly recessive lethal mutations. Overall, evolution towards higher sexual reproduction is hindered at low sexual reproduction rates and intermediate selfing rates, but favored under high selfing rates. The results suggest that asexual reproduction may precede the evolution of selfing, and offer insights into the evolution of mechanisms reducing geitonogamy in partially clonal populations.

evolutionary biology↗

bioRxiv2023

Evolution of flowering time through the asynchrony of pollen dispersal

The evolution of flowering time is often attributed to variation of pollinator rates over time. This study proposes that flowering time can evolve through siring success variation among individuals caused by differential pollen dispersal timing (a result of flowering time variation itself). Quantitative genetic models show that earlier flowering evolves under low pollen removal rates, high pollen deposition rates, and a slow decline in the fertilization ability of removed pollen. Variations in pollen dispersal timing also select for a stable variance in flowering time, which is larger when pollen removal rates are either very low or high, pollen deposition rates are moderate, and the fertilization ability of removed pollen declines more rapidly. Also, a model on the coevolution of flower longevity and flowering time predicts that under constant pollination rates, non-random mating results in a weak correlation between late flowering and longer-lived flowers. This baseline finding suggests that the observed correlation between late flowering and shorter flowering duration in nature is influenced by other factors, such as declining pollination rates during late-stage flowering. I discuss the role of altered pollination rates under climate change during flowering time evolution and the importance of distinguishing between pollen removal and deposition rates.

evolutionary biology↗

bioRxiv2023

Asymmetric oligomerization state and sequence patterning can tune multiphase condensate miscibility

Endogenous biomolecular condensates, comprised of a multitude of proteins and RNAs, can organize into multiphasic structures, with compositionally-distinct phases. This multiphasic organization is generally understood to be critical for facilitating their proper biological function. However, the biophysical principles driving multiphase formation are not completely understood. Here, we utilize in vivo condensate reconstitution experiments and coarse-grained molecular simulations to investigate how oligomerization and sequence interactions modulate multiphase organization in biomolecular condensates. We demonstrate that increasing the oligomerization state of an intrinsically disordered protein region (IDR) results in enhanced immiscibility and multiphase formation. Interestingly, we found that oligomerization tunes the miscibility of IDRs in an asymmetric manner, with the effect being more pronounced when the IDR exhibiting stronger homotypic IDR interactions is oligomerized. Our findings suggest that oligomerization is a flexible biophysical mechanism which cells can exploit to tune the internal organization of biomolecular condensates and their associated biological functions.

biophysics↗

bioRxiv2023

LINC01117 inhibits invasion and migration of lung adenocarcinoma through influencing EMT process

BackgroundStudying the mechanism of action of LincRNAs in lung adenocarcinoma (LUAD) is of great importance for an in-depth understanding of the molecular mechanism of lung adeno carcinogenesis and development. ObjectiveTo identify long-stranded non-coding RNAs that are specifically highly expressed in LUAD cells and to investigate their function in LUAD cells to provide new potential targets for targeting LUAD therapy. MethodsThis study used publicly available data downloaded from The Cancer Genome Atlas (TCGA) database. Construction of siRNA and overexpression plasmid-packed lentiviral constructs were used to knock down and increase the expression of LINC01117 in LUAD cells. The effect of LINC01117 on LUAD cell migration and invasion was verified by scratch assays and Transwell assays. Western blot assays were performed to verify the effect of knocking down LINC01117 expression on key proteins of the EMT process. ResultsLINC01117 expression was upregulated in LUAD tissues and cell lines. Clinical correlation and prognostic analyses showed that LINC01117 was associated with poorer clinical features (staging and N classification) and poorer prognosis and could be analyzed as an independent prognostic factor. Cell migration and invasion were significantly inhibited in the knockdown group compared to the control group; in contrast, cell migration and invasion were promoted in the overexpression group. The expression of N-cadherin and vimentin, molecular markers of the EMT process, was elevated in the overexpression group, and the expression of E-cadherin was decreased. Conclusions: LINC01117 was highly expressed in LUAD cells, and inhibition of LINC01117 expression significantly inhibited the migration and invasion of LUAD cells, while overexpression of LINC01117 significantly promoted the migration and invasion of LUAD cells, and may affect the migration ability of LUAD cells through the EMT process. It suggests that LINC01117 may play a key role in the occurrence and development of LUAD.

molecular biology↗

bioRxiv2023

Ferroptosis is determined by chloride ions

Ferroptosis has emerged as a deliberate type of programmed cell death that manifests marked importance ubiquitously in health and diseases. However, after a decade of research, the mechanisms of ferroptosis execution remain unclear. Here we identify chloride ions (Cl-) as essential determinants of ferroptosis. Water homeostasis manipulated by extracellular solute concentration disrupts ferroptotic cell death. Hyperosmotic stress attenuates ferroptosis and endues cells with high lipid peroxidation. Analyses of a fluorescent chloride probe show that Cl- fluxes into the cytoplasm during ferroptosis, substantiating a role for Cl- to drive water flow. Depletion of extracellular chloride ions ([Cl-]o) from culture media congruously confers resistance to ferroptosis. The [Cl-]o-depleted ferroptotic cells fall into two populations: cells with low lipid peroxidation; cells with high lipid peroxidation but not cell swelling or cell rupture. Contrarily, solitary [Cl-]o overload is sufficient to elicit ferroptosis without canonical ferroptosis inducers. Further experiments show that ferroptotic cells depolarize and [Cl-]o is positively correlated with this process. Membrane depolarization upregulates the level of lipid peroxidation, suggesting that membrane potential may be a universal mechanism governing ferroptosis. Together, our findings reveal that ferroptosis is determined by chloride ions.

cell biology↗

bioRxiv2023

Single-molecule displacement mapping indicates unhindered intracellular diffusion of small (<~1 kDa) solutes

While fundamentally important, the intracellular diffusion of small (<~1 kDa) solutes has been difficult to elucidate due to challenges in both labeling and measurement. Here we quantify and spatially map the translational diffusion patterns of small solutes in mammalian cells by integrating several recent advances. In particular, by executing tandem stroboscopic illumination pulses down to 400-s separation, we extend single-molecule displacement/diffusivity mapping (SMdM), a super-resolution diffusion quantification tool, to small solutes with high diffusion coefficients D of >300 m2/s. We thus show that for multiple water-soluble dyes and dye-tagged nucleotides, intracellular diffusion is dominated by vast regions of high diffusivity ~60-70% of that in vitro, up to ~250 m2/s in the fastest cases. Meanwhile, we also visualize sub-micrometer foci of substantial slowdowns in diffusion, thus underscoring the importance of spatially resolving the local diffusion behavior. Together, these results suggest that the intracellular diffusion of small solutes is only modestly scaled down by the slightly higher viscosity of the cytosol over water, but otherwise not further hindered by macromolecular crowding. We thus lift a paradoxically low speed limit for intracellular diffusion suggested by previous experiments. Abstract Graphic O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

biophysics↗

bioRxiv2023

Single-molecule displacement mapping unveils sign-asymmetric protein charge effects on intraorganellar diffusion

Using single-molecule displacement/diffusivity mapping (SMdM), an emerging super-resolution microscopy method, here we quantify, at nanoscale resolution, the diffusion of a typical fluorescent protein (FP) in the endoplasmic reticulum (ER) and mitochondrion of living mammalian cells. We thus show that the diffusion coefficients D in both organelles are ~40% of that in the cytoplasm, with the latter exhibiting higher spatial inhomogeneities. Moreover, we unveil that diffusions in the ER lumen and the mitochondrial matrix are markedly impeded when the FP is given positive, but not negative, net charges. Calculation shows most intraorganellar proteins as negatively charged, thus a mechanism to impede the diffusion of positively charged proteins. However, we further identify the ER protein PPIB as an exception with a positive net charge, and experimentally show that the removal of this positive charge elevates its intra-ER diffusivity. We thus unveil a sign-asymmetric protein charge effect on the nanoscale intraorganellar diffusion.

biophysics↗

bioRxiv2023

Accurate and interpretable gene expression imputation on scRNA-seq data using IGSimpute

Single-cell RNA-sequencing (scRNA-seq) enables the quantification of gene expression at the transcriptomic level with single-cell resolution, enhancing our understanding of cellular heterogeneity. However, the excessive missing values present in scRNA-seq data (termed dropout events) hinder downstream analysis. While numerous imputation methods have been proposed to recover scRNA-seq data, high imputation performance often comes with low or no interpretability. Here, we present IGSimpute, an accurate and interpretable imputation method for recovering missing values in scRNA-seq data with an interpretable instance-wise gene selection layer. IGSimpute outperforms ten other state-of-the-art imputation methods on nine tissues of the Tabula Muris atlas with the lowest mean squared error as the chosen benchmark metric. We demonstrate that IGSimpute can give unbiased estimates of the missing values compared to other methods, regardless of whether the average gene expression values are small or large. Clustering results of imputed profiles show that IGSimpute offers statistically significant improvement over other imputation methods. By taking the heart-and-aorta and the limb muscle tissues as examples, we show that IGSimpute can also denoise gene expression profiles by removing outlier entries with unexpected high expression values via the instance-wise gene selection layer. We also show that genes selected by the instance-wise gene selection layer could indicate the age of B cells from bladder fat tissue of the Tabula Muris Senis atlas. IGSimpute has linear time-complexity with respect to cell number, and thus applicable to large datasets.

bioinformatics↗

bioRxiv2023

Extraordinary Evasion of Neutralizing Antibody Response by Omicron XBB.1.5, CH.1.1 and CA.3.1 Variants

Newly emerging Omicron subvariants continue to emerge around the world, presenting potential challenges to current vaccination strategies. This study investigates the extent of neutralizing antibody escape by new subvariants XBB.1.5, CH.1.1, and CA.3.1, as well as their impacts on spike protein biology. Our results demonstrated a nearly complete escape of these variants from neutralizing antibodies stimulated by three doses of mRNA vaccine, but neutralization was rescued by a bivalent booster. However, CH.1.1 and CA.3.1 variants were highly resistant to both monovalent and bivalent mRNA vaccinations. We also assessed neutralization by sera from individuals infected during the BA.4/5 wave of infection and observed similar trends of immune escape. In these cohorts, XBB.1.5 did not exhibit enhanced neutralization resistance over the recently dominant BQ.1.1 variant. Notably, the spike proteins of XBB.1.5, CH.1.1, and CA.3.1 all exhibited increased fusogenicity compared to BA.2, correlating with enhanced S processing. Overall, our results support the administration of new bivalent mRNA vaccines, especially in fighting against newly emerged Omicron subvariants, as well as the need for continued surveillance of Omicron subvariants.

microbiology↗

bioRxiv2023

Leafhopper transmits soybean stay-green associated virus to legume plants

A novel geminivirus, soybean stay-green associated virus (SoSGV), was previously shown to cause soybean delayed senescence and is associated with the incidences of soybean stay-green syndrome. The transmission methods of SoSGV were not yet understood. We captured insects belonging to 24 distinct species in a soybean field with the SoSGV outbreak and detected the presence of SoSGV only in leafhoppers and bean bugs (Riptortus pedestris). Caged feeding experiments using captured leafhoppers and bean bugs from soybean fields showed that leafhoppers, but not bean bugs, are vectors transmitting SoSGV. The common brown leafhopper (Orosius orientalis) is identified as the dominant leafhopper species and can establish colonies feeding on soybean plants in experimental conditions. An investigation of SoSGV defective DNA revealed that soybean genomic DNA could be inserted into the SoSGV genome, while sequences from wild soybean, red bean, and cowpea were also identified. We further showed that the common brown leafhopper could transmit SoSGV to wild soybean and red bean plants, emphasizing the vector role of the leafhopper in the transmission of SoSGV in the field.

microbiology↗

bioRxiv2022

Structural insights into human ABCC4 mediated transport of platelet agonist and inhibitor

The activation and accumulation of human platelets contributes to hemostasis and thrombosis, the imbalance of which would cause cardiovascular diseases, an increasing threat to the global health. Human ABC transporter ABCC4 that pumps out the platelet agonist and anti-platelet drug such as aspirin, might become a promising target for preventing cardiovascular diseases. Here we solve the structures of human ABCC4 in the apo and two complexed forms, all of which adopt a typical architecture of type-IV ABC transporters in an inward-facing conformation. Structure of ABCC4 complexed with U46619, an analog of the unstable TXA2, provides the first structural evidence that the platelet agonist TXA2 is also exported via ABCC4. The dipyridamole-complexed structure reveals the inhibitory mechanism of dipyridamole against ABCC4. Structural comparisons enabled us to identify a transmembrane pocket in ABCC4 that provides a defined space for the rational design of specific anti-platelet drugs.

biochemistry↗

bioRxiv2022

Neurodegeneration Risk Factor, EIF2AK3 (PERK), Influences Tau Protein Aggregation

Tauopathies are neurodegenerative diseases caused by pathologic misfolded tau protein aggregation in the nervous system. Population studies implicate EIF2AK3 (eukaryotic translation initiation factor 2 alpha kinase 3), better known as PERK (protein kinase R-like endoplasmic reticulum kinase), as a genetic risk factor in several tauopathies. PERK is a key regulator of intracellular proteostatic mechanisms - Unfolded Protein Response (UPR) and Integrated Stress Response (ISR). Previous studies found that tauopathy-associated PERK variants encoded functional hypomorphs with reduced signaling in vitro. But, it remained unclear how altered PERK activity led to tauopathy. Here, we chemically or genetically modulated PERK signaling in cell culture models of tau aggregation and found that PERK pathway activation prevented tau aggregation while inhibition exacerbated tau aggregation. In primary tauopathy patient brain tissues, we found that reduced PERK signaling correlated with increased tau neuropathology. We found that tauopathy-associated PERK variants targeted the ER luminal domain; and two of these variants damaged hydrogen bond formation. Our studies support that PERK activity protects against tau aggregation and pathology. This may explain why people carrying hypomorphic PERK variants have increased risk for developing tauopathies. Finally, our studies identify small molecule augmentation of PERK signaling as an attractive therapeutic strategy to treat tauopathies by preventing tau pathology.

neuroscience↗

bioRxiv2022

NR5A2 connects genome activation to the first lineage segregation in early mouse development

After fertilization, zygotic genome activation (ZGA) marks the beginning of the embryonic program for a totipotent embryo, which further gives rise to the pluripotent embryonic lineages and extraembryonic trophectoderm after the first lineage commitment. While much has been learned about pluripotency regulation, how ZGA is connected to the pluripotency commitment in early embryos remains elusive. Here, we investigated the role of nuclear receptor 1 family transcription factors (TFs) in mouse pre-implantation embryos, whose motifs are highly enriched in accessible chromatin at the 2-cell (2C) to 8-cell (8C) stages after ZGA. We found NR5A2, an NR TF highly induced upon ZGA, is required for early development, as both the knockdown and knockout of Nr5a2 from 1C embryos led to morula arrest. While the zygotic genome was largely activated at the 2C stage, 4-8C-specific gene activation (mid-preimplantation activation) was substantially impaired. Genome-wide chromatin binding and RNA-seq analyses showed NR5A2 preferentially regulates its binding targets including a subset of key pluripotency genes (i.e., Nanog, Pou5f1, and Tdgf1). Finally, NR5A2-occupied sites at the 2C and 8C stages predominantly reside in accessible B1 elements where its motif is embedded. Taken together, these data identify NR5A2 as a key regulator that connects ZGA to the first lineage segregation in early mouse development.

developmental biology↗

bioRxiv2022

TRPV1-mediated sonogenetic neuromodulation of motor cortex in freely moving mice

BackgroundNoninvasive and cell-type-specific neuromodulation tools are critically needed for probing intact brain function. Sonogenetics for noninvasive activation of neurons engineered to express thermosensitive transient receptor potential vanilloid 1 (TRPV1) by transcranial focused ultrasound (FUS) was recently developed to address this need. However, using TRPV1-mediated sonogenetics to evoke behavior by targeting the cortex is challenged by its proximity to the skull due to high skull absorption of ultrasound and increased risks of thermal-induced tissue damage. ObjectiveThis study evaluated the feasibility and safety of TRPV1-mediated sonogenetics in targeting the motor cortex to modulate the locomotor behavior of freely moving mice. MethodsAdeno-associated virus was delivered to the mouse motor cortex via intracranial injection to express TRPV1 in excitatory neurons. A wearable FUS device was installed on the mouse head after a month to control neuronal activity by activating virally expressed TRPV1 through FUS sonication at different acoustic pressures. Immunohistochemistry staining of ex vivo brain slices was performed to verify neuron activation and evaluate safety. ResultsTRPV1-mediated sonogenetic stimulation at 0.7 MPa successfully evoked rotational behavior in the direction contralateral to the stimulation site, activated cortical neurons as indicated by the upregulation of c-Fos, and did not induce significant changes in inflammatory or apoptotic markers (GFAP, lba1, and Caspase-3). Sonogenetic stimulation of TRPV1 mice at a higher acoustic pressure, 1.1 MPa, induced significant changes in motor behavior and upregulation of c-Fos compared with FUS sonication of naive mice at 1.1 MPa. However, signs of damage at the meninges were observed at 1.1 MPa. ConclusionsTRPV1-mediated sonogenetics can achieve effective and safe neuromodulation at the cortex with carefully selected FUS parameters. These findings expand the application of this technique to include superficial brain targets.

bioengineering↗

bioRxiv2022

Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions

Transcription factors (TFs) activate enhancers to drive cell-specific gene programs in response to signals, but our understanding of enhancer assembly during signaling events is incomplete. Here, we show that Androgen Receptor (AR), a steroid hormone-regulated transcription factor, forms condensates through multivalent interactions in response to androgen signaling to orchestrate enhancer assembly. We demonstrate that the intrinsically disordered N-terminal domain (NTD) of AR drives 1,6-Hexanediol-sensitive condensate formation and that NTD deletion or aromatic residue mutation reduces AR self-association and abolishes AR transcriptional activity. AR NTD can be substituted by intrinsically disordered regions (IDRs) from selective proteins for AR condensation capacity and transactivation function. Surprisingly, strengthened AR condensation capacity caused by extending the polyQ tract within AR NTD also leads to impaired transcriptional activity without affecting AR binding on enhancers. Furthermore, either NTD deletion or polyQ extension reduces heterotypic multivalent interactions between AR and other enhancer components. These results suggest the importance of an optimal level of AR condensation in mediating AR-AR homotypic and AR-cofactor heterotypic interactions to regulate enhancer assembly in response to signals. Our study supports the notion that alteration of the fine-tuned multivalent IDR-IDR interactions might underlie AR-related human pathologies, thereby providing novel molecular insights for potential therapeutic strategies to treat prostate cancer and other AR-involved diseases by targeting AR multivalent interactions.

molecular biology↗

bioRxiv2022

NanoBlot: A Simple Tool for Visualization of RNA Isoform Usage From Third Generation RNA-sequencing Data

RT-PCR and Northern blots have long been used to study RNA isoforms usage for single genes. Recently, advancements in long read sequencing have yielded unprecedented information about the usage and abundance of these RNA isoforms. However, visualization of long-read sequencing data remains challenging due to the high information density. To alleviate these issues we have developed NanoBlot, a simple, open-source, command line tool, which generates Northern blot and RT-PCR-like images from third generation sequencing data. NanoBlot accepts processed bam files. Plotting is based around ggplot2 and is easily customizable. Advantages of NanoBlots include: designing probes to visualize isoforms which would be impossible with traditional RT-PCR or Northern blots, excluding reads from the Nanoblots based on the presence or absence of a specified region and, multiplexing plots with multiple colors. We present examples of NanoBlots compared to actual northern blot data. In addition to traditional gel-like images, NanoBlot also outputs other visualizations such as violin plots. The use of Nanoblot should provide a simple answer to the challenge of visualization of long-read RNA sequencing data.

bioinformatics↗