Biology subjects

Zhou, X.

Publications and source records attributed to Zhou, X..

At least 433 records · Page 24Linked to original sources

bioRxiv2022

Cytoophidia safeguard binucleation of Drosophila male accessory gland cells

Although most cells are mononuclear, the nucleus can exist in the form of binucleate or even multinucleate to respond to different physiological processes. The male accessory gland of Drosophila is the organ that produces semen, and its main cells are binucleate. Here we observe that CTP synthase (CTPS) forms filamentous cytoophidia in binuclear main cells, primarily located at the cell boundary. In CTPSH355A, a point mutation that destroys the formation of cytoophidia, we find that the nucleation mode of the main cells changes, including mononucleates and vertical distribution of binucleates. Although the overexpression of CTPSH355A can restore the level of CTPS protein, it will neither form cytoophidia nor eliminate the abnormal nucleation pattern. Therefore, our data indicate that there is an unexpected functional link between the formation of cytoophidia and the maintenance of binucleation in Drosophila main cells.

developmental biology↗

bioRxiv2022

The genomes of medicinal skullcaps reveal the polyphyletic origins of clerodane diterpene biosynthesis in the family Lamiaceae.

The presence of anticancer clerodane diterpenoids is a chemotaxonomic marker for the traditional Chinese medicinal plant Scutellaria barbata, although the molecular mechanisms behind clerodane biosynthesis are unknown. Here, we report a high-quality assembly of the 414.98 Mb genome of S. barbata into thirteen pseudochromosomes. Using phylogenomic and biochemical data, we mapped the plastidial metabolism of kaurene (gibberellins), abietane and clerodane diterpenes in three species of the family Lamiaceae (Scutellaria barbata, Scutellaria baicalensis and Salvia splendens), facilitating the identification of genes involved in the biosynthesis of the clerodanes, kolavenol and isokolavenol. We show that clerodane biosynthesis evolved through recruitment and neofunctionalization of genes from gibberellin and abietane metabolism. Despite the assumed monophyletic origin of clerodane biosynthesis which is widespread in species of the Lamiaceae, our data show distinct evolutionary lineages and suggest polyphyletic origins of clerodane biosynthesis in the family Lamiaceae. Our study not only provides significant insights into the evolution of clerodane biosynthetic pathways in the mint family, Lamiaceae, but also will facilitate the elucidation of anticancer clerodanes biosynthesis and future metabolic engineering efforts to increase the production of these high-value chemicals.

plant biology↗

bioRxiv2022

GTP as an enzymatic synchronizer

CTP synthase (CTPS), the sole enzyme for de novo CTP biosynthesis, requires GTP as an allosteric effector for efficient catalysis1. Although the labile intermediates and chemical reaction steps have been characterized, how CTPS coordinates its structural domains through interactions with GTP to continuously catalyze thus reactions and thereby synthesize CTP correctly remains elusive. Through cryo-EM analysis of 34 structural states (2.0-3.3 [A] resolution) spanning pre-catalytic, catalytic, and post-catalytic conformations, we delineate how GTP cycling--intact binding and dissociation--directly gates three sequential activation checkpoints. 1) Catalytic initiation gate: GTP dissociation precedes substrate entry, transitioning CTPS to a substrate-competent state. 2) Intermediate-dependent GTP recruitment: 4Pi-UTP formation allosterically remodels the GAT domain, licensing GTP rebinding. 3) Ammonia transfer gate: GTP directly constitutes the transient interdomain gas tunnel for ammonia delivery while stimulating the glutamine hydrolyzing. CTP synthesis completion triggers GTP dissociation, allowing glutamate release. Each catalytic cycle couples CTP production to a single GTP-binding event, demonstrating that GTP cycling operates as a catalytic-phase timer. This work provides a comprehensive model for the efficient catalysis of CTPS and establishes effector cycling as a dynamic gating mechanism in enzymes.

biochemistry↗

bioRxiv2022

DNA damage response signaling to mitochondria drives senescence

Cellular senescence is a stress-induced irreversible cell cycle arrest typically accompanied by expression of the cyclin-dependent kinase inhibitor p16INK4a (hereafter referred to as p16) and mitochondrial dysfunction1. Recent studies have indicated that p16-expressing senescent cells accumulate in the body over time and contribute to aging1, 2. Many stresses, such as telomere shortening and oncogene activation, induce senescence by damaging nuclear DNA1. However, the molecular mechanisms linking DNA damage to senescence remain unclear. Here, we show that the outer mitochondrial transmembrane protein BNIP3 drives senescence by triggering a DNA damage response (DDR) of mitochondria. BNIP3 was identified in a genome-wide siRNA screen for genes required for p16 expression upon DNA damage. Mass spectrometric analysis of BNIP3-interacting proteins yielded the DDR kinase ATM and subunits of the mitochondrial contact site and cristae organizing system (MICOS) complex. BNIP3 is an ATM substrate that increases the number of mitochondrial cristae upon DNA damage. This increase enhances the oxidation of fatty acids to acetyl-CoA, an acetyl group donor, thereby promoting histone acetylation and associated p16 expression. Our findings indicate that DDR signaling to mitochondria promotes p16 expression by altering mitochondrial structure and metabolism and highlight the importance of nuclear-mitochondrial communication in senescence induction.

cell biology↗

bioRxiv2022

Dysregulation of mTOR Signaling Mediates Common Neurite and Migration Defects in Both Idiopathic and 16p11.2 Deletion Autism Neural Precursor Cells

Autism spectrum disorder (ASD) is defined by common behavioral characteristics, raising the possibility of shared pathogenic mechanisms. Yet, vast clinical and etiological heterogeneity suggests personalized phenotypes. Surprisingly, our iPSC studies find that six individuals from two distinct ASD-subtypes, idiopathic and 16p11.2 deletion, have common reductions in neural precursor cell (NPC) neurite outgrowth and migration even though whole genome sequencing demonstrates no genetic overlap between the datasets. To identify signaling differences that may contribute to these developmental defects, an unbiased phospho-(p)-proteome screen was performed. Surprisingly despite the genetic heterogeneity, hundreds of shared p-peptides were identified between autism subtypes including the mTOR pathway. mTOR signaling alterations were confirmed in all NPCs across both ASD-subtypes, and mTOR modulation rescued ASD phenotypes and reproduced autism defects in controls. Thus, our studies demonstrate that genetically distinct ASD subtypes have common defects in neurite outgrowth and migration which are driven by the shared pathogenic mechanism of mTOR signaling dysregulation.

neuroscience↗

bioRxiv2022

Cuproptosis is correlated with clinical status, tumor immune microenvironment and immunotherapy in colorectal cancer: a multi-omic analysis

Copper, like double-edged sword, either too little or too much can lead to cell death. Cuproptosis, a novel identified cell death form induced by copper, is characterized by aggregation of lipoylated mitochondrial enzymes and the destabilization of Fe-S cluster proteins. However, the function and potential clinical value of cuproptosis in colorectal cancer remains largely unknown. In this study, 16 cuproptosis-related molecules (CPRMs) were identified and analyzed by transcriptomics, genomics, and single-cell transcriptome profiling from multiple databases. We established two cuproptosis-related molecular phenotypes (CMP1 and 2) to distinguish CRC individuals, in which there were significantly differences in prognosis, biological function, somatic mutation frequency, immune cell infiltration in CRC individuals. A novel cuproptosis-related scoring system (CuproScore) was also constructed to predict the prognosis of CRC individuals, TME and the response to immunotherapy. Of notion, the value of CuproScore was also confirmed in our transcriptome cohort, demonstrating that CRC individuals in the high CuproScore group tended to have higher immune cell infiltrations and higher immune checkpoint expression. We also checked and analyzed the expression and clinical significance of 16 CPRMs in CRC cell lines and CRC tissues. This study indicated that cuproptosis and CPRMs played significant role in CRC progression and in modeling the TME. Inducing cuproptosis may be a useful tool for tumor therapy in the future.

cancer biology↗

bioRxiv2022

Dissociated amplitude and phase effects of alpha oscillation in a nested structure of rhythm- and sequence-based temporal expectation

The human brain can utilize various information to form temporal expectation and optimize perceptual performance. Here we show dissociated amplitude and phase effects of pre-stimulus alpha oscillation in a nested structure of rhythm- and sequence-based expectation. A visual stream of rhythmic stimuli was presented in a fixed sequence such that their temporal positions could be predicted by either the low-frequency rhythm, the sequence, or the combination. The behavioral modelling indicated that rhythmic and sequence information additively led to increased accumulation of sensory evidence and alleviated threshold for the perceptual discrimination of the expected stimulus. The electroencephalographical (EEG) results showed that the alpha amplitude was dominated by rhythmic information, with the amplitude fluctuating in the same frequency of the oscillation entrained by the rhythmic information (i.e., phase-amplitude coupling). The alpha phase, however, was affected by both rhythmic and sequence information. Importantly, rhythm-based expectation improved the perceptual performance by decreasing the alpha amplitude, whereas sequence-based expectation did not further decrease the amplitude on top of rhythm-based expectation. Moreover, rhythm-based and sequence-based expectation collaboratively improved the perceptual performance by biasing the alpha oscillation toward the optimal phase. Our findings suggested flexible coordination of multiscale brain oscillations in dealing with a complex environment.

neuroscience↗

bioRxiv2022

Predicting anti-cancer drug synergy using extended drug similarity profiles

Combination therapy is a promising strategy for confronting the complexity of cancer. However, experimental exploration of the vast space of potential drug combinations is costly and unfeasible. Therefore, computational methods for predicting drug synergy are much-needed for narrowing down this space, especially when examining new cellular contexts. Here, we thus introduce CCSynergy, a flexible, context-aware and integrative deep learning framework that we have established to unleash the potential of the Chemical Checker extended drug similarity profiles for the purpose of drug synergy prediction. We have shown that CCSynergy enables predictions of superior accuracy, remarkable robustness and improved context-generalizability as compared to the state-of-the-art methods in the field. Having established the potential of CCSynergy for generating experimentally validated predictions, we exhaustively explored the untested drug combination space. This resulted in a compendium of potentially synergistic drug combinations on hundreds of cancer cell lines, which can guide future experimental screens.

bioinformatics↗

bioRxiv2022

Depolarization of astrocytes in the basolateral amygdala restores WFS1 neuronal activity and rescues impaired risk-avoidance behavior in DISC1TM mice

Many mental illnesses are accompanied by abnormal risk-avoidance behavior, yet we have only a limited understanding of the neuronal regulatory mechanisms involved. We previously established an inducible DISC1-N terminal fragment transgenic mouse (DISC1-NTM) model which has exhibited risk-avoidance deficiency. Using this model, we analyzed differentially expressed genes (DEGs) using snRNA-seq and the results indicate impaired neuron-astrocyte interactions. We used optogenetic tools to modulate astrocytes in the basolateral amygdala (BLA) and found that ChR2-expressing astrocytes were able to rescue risk-avoidance impairment in DISC1-NTM mice. Using patch clamp recordings combined with signal-cell qPCR, we found impaired excitability of BLAWFS1 neurons in DISC1-NTM mice and that ChR2-expressing astrocytes can induce action potentials (APs) in WFS1 neurons, which restores WFS1 neuronal activity. WFS1 neurons are necessary for BLA astrocytes to modulate impaired risk-avoidance behavior. These finding provide new insights into mechanisms of astrocyte-neuron interactions and suggest that BLA astrocytes may be a promising target for impaired risk avoidance in mental illness. HighlightsChR2-expressing astrocytes in the BLA rescue impaired risk-avoidance behavior in DISC1-NTM mice. Astrocytes in the BLA modulate different nearby neurons to different degrees. Depolarization of BLA astrocytes restore neuronal activity in WFS1 neurons. Astrocytes in the BLA modulate WFS1 neurons via NMDARs.

neuroscience↗

bioRxiv2022

A Peronophythora litchii RXLR effector PlAvh202 enhances plant susceptibility by destabilizing host SAMS

Oomycete pathogens can secret hundreds of effectors into plant cells to interfere with plant immune system during infection. Here we identified a cytoplasmic RXLR effector from the most destructive pathogen of litchi, Peronophythora litchii, and named it as PlAvh202. PlAvh202 could suppress cell death triggered by INF1 and Avr3a/R3a in Nicotiana benthamiana, and was essential for P. litchii virulence. In addition, PlAvh202 also suppressed plant immune responses and promoted the susceptibility of N. benthamiana to Phytophthora capsici. Further research revealed that PlAvh202 could suppress ethylene (ET) production by targeting and destabilizing plant S-adenosyl-L-methionine synthetase (SAMS), a key enzyme in ET biosynthesis pathway, in a 26S proteasome-dependent manner. Transient expression of LcSAMS3 induced ET production and enhanced plant resistance, whereas inhibition of ET biosynthesis promoted P. litchii infection, supporting that LcSAMS and ET positively regulate litchi immunity towards P. litchii. Overall, these findings highlight that SAMS can be targeted by oomycete RXLR effector to manipulate ET-mediated plant immunity.

plant biology↗

bioRxiv2022

Age-dependent changes in the dynamic functional organization of the brain at rest - a cross - cultural replication approach

Age-associated changes in brain function play an important role in the development of neurodegenerative diseases. Although previous work has examined age-related changes in static functional connectivity (FC), accumulating evidence suggests that advancing age is especially associated with alterations in the dynamic interactions and transitions between different brain states, which hitherto has received less attention. Moreover, conclusions of previous studies in this domain are limited by suboptimal replicability of resting state fMRI and culturally homogenous cohorts. Here, we investigate the robustness of age-associated changes in dynamic functional connectivity (dFC) by capitalizing on the availability of fMRI cohorts from two cultures (Western European and Chinese). In both cohorts we consistently identify two distinct connectivity states: a more frequent segregated within-network connectivity state (state I) and a less frequent integrated between-network connectivity state (state II). In both cohorts, older (55-80 years) compared to younger participants (20-35 years) exhibited lower occurrence of and spent less time in state I. Moreover, older participants tended to exhibit more transitions between networks and greater variance in global efficiency. Overall, our cross-cultural replication of age-associated changes in key dFC metrics implies that advancing age is robustly associated with a reorganization of dynamic brain activation that favors the use of less functionally-specific networks. HighlightsAging is associated with a reorganization of dynamic functional brain connectivity. Age-dependent dynamic functional connectivity changes are relatively stable across cultures. Dynamic properties are promising neural indexes for brain aging in older healthy populations.

neuroscience↗

bioRxiv2022

IL-22/IL-22RA1 promotes human Tenon's capsule fibroblasts proliferation and regulates fibrosis through STAT3 signaling pathway

The study is aimed to investigate that the IL-22/IL-22RA1 signaling pathway regulates scar formation. A total of 31 glaucoma patients who had been previously treated with trabeculectomy surgery and the intraocular pressure was uncontrollable because of scarring and 19 strabismus patients as control patient group. ELISA showed that the IL-22 content of serum from glaucoma patients was 29.80{+/-}5.1 ng/l which is higher than that 5.21{+/-}0.9 ng/l from healthy group significantly. Serum from patients was used to incubate human Tenons capsule fibroblasts (HTFs) cells and IL-22 antibody rescued the effect of IL-22 on the biological functions. qPCR and western blot result showed that IL-22 mediates the biological function of HTFs cells via binding IL-22RA1 directly. When transfection of siR-IL-22RA1 or IL-22RA1 gene, the HTFs cells shown significantly anti-fibrosis or pro-fibrosis separately. By using STAT3 inhibitor BAY in IL-22RA1 overexpression group, IL-22-induced proliferation were reduced in HTFS cells. IL-22 promoted fibroblasts cell proliferation and -SMA via IL-22/IL-22RA1/STAT3 signaling pathway, thereby potentially regulating glaucoma filtration trace fibrosis. This results also show the novel factor in process of postoperative scarring. Summary StatementThe present study suggested that IL-22 expression in glaucoma patient after surgery. IL-22/IL-22RA1 signaling pathway promoted fibroblasts cell proliferation and -SMA by activating the STAT3 signaling pathway, thereby potentially regulating glaucoma filtration trace fibrosis.

cell biology↗

bioRxiv2022

Simultaneous Profiling of Host Expression and Microbial Abundance by Spatial Meta-Transcriptome Sequencing

We developed an analysis pipeline that can extract microbial sequences from Spatial Transcriptomic (ST) data and assign taxonomic labels, generating a spatial microbial abundance matrix in addition to the default host expression matrix, enabling simultaneous analysis of host expression and microbial distribution. We called the pipeline Spatial Meta-transcriptome (SMT) and applied it on both human and murine intestinal sections and validated the spatial microbial abundance information with alternative assays. Biological insights were gained from this novel data that demonstrated host-microbe interaction at various spatial scales. Finally, we tested experimental modification that can increase microbial capture while preserving host spatial expression quality, and by use of positive controls, quantitatively demonstrated the capture efficiency and recall of our methods. This proof of concept work demonstrates the feasibility of Spatial Meta-transcriptomic analysis, and paves the way for further experimental optimization and application.

genomics↗

bioRxiv2022

Genetically encoded photocatalytic protein labeling enables spatially-resolved profiling of intracellular proteome

Mapping the subcellular organization of proteins is crucial for understanding their biological functions. Herein, we report a reactive oxygen species induced protein labeling and identification (RinID) method for profiling subcellular proteome in the context of living cells. Our method capitalizes on a genetically encoded photocatalyst, miniSOG, to locally generate singlet oxygen that reacts with proximal proteins. Labeled proteins are conjugated in situ with an exogenously supplied nucleophilic probe, which serves as a functional handle for subsequent affinity enrichment and mass spectrometry-based protein identification. From a panel of nucleophilic compounds, we identify biotin-conjugated aniline and propargyl amine as highly reactive probes. As a demonstration of the spatial specificity and depth of coverage in mammalian cells, we apply RinID in the mitochondrial matrix, capturing 394 mitochondrial proteins with 97% specificity. We further demonstrate the broad applicability of RinID in various subcellular compartments, including the nucleus and the endoplasmic reticulum.

biochemistry↗

bioRxiv2022

Discovery of unknown quorum-sensing reprogramming factors in Pseudomonas aeruginosa using a dual-acting-gene-blocking approach

LasR is a master regulator of quorum-sensing (QS) in Pseudomonas aeruginosa. LasR-null mutants commonly appear in lung isolates from chronically infected cystic fibrosis (CF) patients. However, numerous such CF isolates have a QS-active phenotype, but factors underlying QS-reprogramming in LasR-null mutants remain largely unknown. Mutations in the transcriptional regulator gene mexT are well known to be responsible for QS-reprogramming in a laboratory LasR-null mutant strain, however, simultaneous occurrence of lasR and mexT mutations is rare in CF isolates. To identify QS-reprogramming determinants, we developed an experimental evolution approach, for which a QS-inactive LasR null mutant with an extra copy of mexT was engineered. In such a strain, spontaneous single mexT mutations are expected to have no or little phenotypic consequences. This novel method, named "targeted gene duplication followed by mutant screening" (TGD-MS), resulted in the identification of QS-active revertants with mutations in genes other than mexT. We characterized a QS-active revertant with a point mutation in rpoA, a gene encoding the -subunit of RNA polymerase. QS activation in this mutant was found to be associated with the down-regulated expression of mexEF-oprN efflux pump genes. Our study therefore uncovers a new functional role for RpoA in regulating QS activity. Furthermore, our results suggest that a regulatory circuit controlling the expression of the mexEF-oprN operon is critical for QS-reprogramming. In conclusion, our study reports on the identification of non-MexT proteins associated with QS-reprogramming in a laboratory strain, shedding light on possible QS activation mechanisms in clinical P. aeruginosa isolates.

microbiology↗

bioRxiv2022

Mixed selectivity coding of content-temporal detail by dorsomedial posterior parietal neurons

The dorsomedial posterior parietal cortex is part of a higher-cognition network implicated in elaborate processes underpinning memory formation, recollection, episodes reconstruction, and temporal information processing. Neural coding for complex episodic processing is however under-documented. Here we revealed a set of neural codes of neuroethogram in the primate parietal cortex. Analyzing neural responses in macaque dmPPC to naturalistic videos, we discovered several groups of neurons that are sensitive to different categories of ethogram-items and to low-level sensory features, and saccadic eye movement. We also discovered that the processing of category and feature information by these neurons is sustained by accumulation of temporal information over a long timescale up to 30 s, corroborating its reported long temporal receptive windows. We performed an additional behavioral experiment and found that saccade-related activities could not account for the mixed neuronal responses elicited by the video stimuli. We further observed monkeys scan-paths and gaze consistency are modulated by video content. Taken altogether, these neural findings explain how dorsomedial PPC weaves fabrics of ongoing experiences together in real-time. The high dimensionality of neural representations should motivate us to shift the focus of attention from pure selectivity neurons to mixed selectivity neurons, especially in increasingly complex naturalistic task designs. HIGHLIGHTSO_LINeural codes for "neuroethogram" in macaque dorsomedial parietal cortex C_LIO_LIParietal neural codes exhibit mixed selectivity of event features C_LIO_LIDorsomedial PPC neurons support a long temporal receptive window for episodes C_LIO_LISaccadic movement could not explain away mixed neuronal responses C_LIO_LIConsistency in scan-path and gaze shown across viewing repetitions C_LI

neuroscience↗

bioRxiv2022

A geometric deep learning framework for drug repositioning over heterogeneous information networks

The effectiveness of computational drug repositioning techniques has been further improved due to the development of artificial intelligence technology. However, most of the existing approaches fall short of taking into account the non-Euclidean nature of biomedical data. To overcome this problem, we propose a geometric deep learning (GDL) framework, namely DDAGDL, to predict drug-disease associations (DDAs) on heterogeneous information networks (HINs). DDAGDL can take advantage of complicated biological information to learn the feature representations of drugs and diseases by ingeniously projecting drugs and diseases including geometric prior knowledge of network structure in a non-Euclidean domain onto a latent feature space. Experimental results show that DDAGDL is able to identify high-quality candidates for Alzheimers disease (AD) and Breast neoplasms (BN) that have already been reported by previously published studies, and some of them are not even identified by comparing models.

bioinformatics↗

bioRxiv2022

Crossmodal reorganization in deaf auditory cortices compensates for the impaired body-centered visuomotor transformation after early deafness

Early deafness leads to the reorganization of large-scale brain networks, involving and extending beyond the auditory system. Body-centered visuomotor transformation is impaired after early auditory deprivation, associated with a hyper-crosstalk between the task-critical frontoparietal network (FPN) and the default-mode network (DMN). It remains to be elucidated, how the reorganized functional connectivity between the auditory system, the FPN, and the DMN contributes to the impaired visuomotor transformation after early deafness. In this fMRI study, we asked early deaf participants and hearing controls to judge the spatial location of a visual target, either about the middle-sagittal line of their own body (the egocentric task) or another background object (the allocentric task). The bilateral superior temporal gyrus (STG) in the deaf group exhibited cross-modal reorganization, with generally enhanced neural activity during the visual tasks, compared to hearing controls. Moreover, the STG showed significantly increased functional connectivity with both the FPN and the DMN in the deaf group compared to hearing controls, specifically during the egocentric task. The increased STG-FPN and STG-DMN coupling, however, showed antagonistic effects on the egocentric performance of the deaf participants. The increased STG-FPN connectivity was associated with improved (i.e., a beneficial role) while the increased STG-DMN with deteriorated (i.e., a detrimental role) egocentric performance in the deaf participants. No such effect was observed in hearing controls. Therefore, the auditory cortex is reorganized to functionally resemble the FPN in the deaf brain, representing compensatory neuroplasticity to mitigate the impaired visuomotor transformation after early deafness. Significance StatementOur brain constantly plans vision-guided actions, transforming visuospatial representations of external visual targets into visuomotor representations. The frontoparietal network (FPN) critically supports this visuomotor transformation process, which is impaired after early deafness. To mitigate the impaired visuomotor transformation, the deaf auditory cortex in the bilateral superior temporal gyrus (STG) shows compensatory cross-modal reorganization that functionally resembles the FPN regions. Specifically, the deaf auditory cortex becomes functionally coupled with the dorsal FPN regions. The stronger the STG-FPN coupling, the more improved the deaf adults visuomotor transformation performance, indicating the reorganized STG as a critical node of the task-critical network. Correspondingly, increased coupling between the task-critical deaf STG and the default-mode network impairs the visuomotor transformation.

neuroscience↗