Biology subjects

Xu, Z.

Publications and source records attributed to Xu, Z..

At least 289 records · Page 16Linked to original sources

bioRxiv2023

Optogenetics reveals roles for supporting cells in force transmission to and from outer hair cells in the mouse cochlea

Cochlear outer hair cells (OHCs), acting as bidirectional cellular mechanoelectrical-transducers, generate, receive, and exchange forces with other major elements of the cochlear partition, including inner hair cells (IHCs). Force exchange is mediated via a supporting cell scaffold, including Deiters (DC) and outer pillar cells (OPC), to enable the sensitivity and exquisite frequency selectivity of the mammalian cochlea. We conditionally expressed a hyperpolarizing halorhodopsin (HOP), a light-gated inward chloride ion pump in DCs and OPCs. We measured extracellular receptor potentials (ERPs) and their DC component (ERPDC) from the Cortilymph (CL) of HOP expressing mice and compared the responses with similar potentials from littermates without HOP expression. Compound action potentials (CAP) were measured as an indication of IHC activity. HOP laser activation suppressed cochlear amplification through changing timing of its feedback, altered basilar membrane (BM) responses to tones at all measured levels and frequencies, and reduced IHC excitation. Our HOP activation results here complement previous channelrhodopsin activation studies in exploiting optogenetics to measure and understand the roles of DCs and OPCs in vivo in controlling the mechanical and electrical responses of OHCs to sound and their contribution to timed and directed electromechanical feedback to the mammalian cochlea. SIGNIFICANCE STATEMENTOuter hair cells provide electromechanical feedback to the organ of Corti, mediated via a cellular scaffold of Deiters and outer pillar cells, that enables the sensitivity and fine frequency tuning of the cochlea. The role of this scaffold was explored by expressing the halorhodopsin HOP in Deiters and pillar cells which, when illuminated, hyperpolarized them. HOP activation suppressed cochlear amplification through altering the timing of outer hair cell forces to the Organ of Corti, altered basilar membrane responses to tones, including those at levels and frequencies not subject to amplification, and reduced neural excitation. The findings implicated roles for supporting cells in mediating force transmission to and from outer hair cells along all axes of the organ of Corti.

neuroscience↗

bioRxiv2023

Unravelling Biosynthesis and Biodegradation Potentials of Microbial Dark Matters in Hypersaline Lakes

Biosynthesis and biodegradation of microorganisms critically underpin the development of biotechnology, new drugs and therapies, and environmental remediation. However, the vast majority of uncultured microbial species along with their metabolic capacities in extreme environments remain obscured. To unravel the metabolic potentials of these microbial dark matters (MDMs), we investigated four deep-inland hypersaline lakes with largely diversified environmental parameters in Xinjiang Uygur Zizhiqu, China. Metagenomic binning obtained 3,030 metagenome-assembled genomes (MAGs) spanning 82 phyla, of which 2,363 MAGs could not be assigned to a known genus. These unknown MAGs were abundantly observed with distinct taxa among lakes, possibly linked to the diversification of physiochemical conditions. Analysis of biosynthetic potentials identified 9,635 biosynthesis gene clusters (BGCs), of which 9,403 BGCs were considered novel. We found that some MAGs from putatively novel phyla consistently comprised enriched BGCs, which may have substantial potentials in biotechnological applications. In addition, biodegradation potentials such as dehalogenation, anaerobic ammonium oxidation (Anammox), polycyclic aromatic hydrocarbon (PAH), and plastic degradation were found in new microbial clades from hypersaline lakes. These findings substantially expanded the genetic repository of biosynthesis and biodegradation potentials, which can further assist the development of new and innovative applications in biotechnology.

microbiology↗

bioRxiv2023

Effect of Acute Stress on Working Memory in Pilots: Investigating the Modulatory Role of Memory Load

The effect of acute stress on working memory (WM) has not been extensively investigated in demanding tasks, although many practitioners, such as pilots, frequently face varying working memory demands. The current study investigated how acute stress modulates pilots WM performance. Forty-two pilots were randomly assigned to the stress group or the control group. The stress group experienced acute stress induced by the modified Trier Social Stress Test (TSST), whereas the control group did not receive any stress induction. Both groups performed N-back tasks under varying degrees of memory load (0-back, 1-back, and 2-back). State-Trait Anxiety Inventory scores, heart rates, and salivary cortisol concentrations were measured in the experiment to determine the extent of induced stress. The results revealed that (1) The modified TSST effectively induced acute stress in the stress group. (2) As rising of memory load, the reaction time expectedly increased while accuracy decreased. (3) An interaction between the stress and control group was found for accuracy, indicating that acute stress might contribute to higher accuracy in moderate WM load (1-back). These suggestions support the emotion regulation hypothesis, in which acute stress induces heightened emotional states that impact WM performance. Furthermore, the current study explored the interplay between acute stress and memory load in a specific population, offering insights into potential pilots stress management strategies and training programs to improve pilots WM abilities. These applications would be beneficial for strengthening pilots coping mechanisms in emergencies and guaranteeing flight safety.

physiology↗

bioRxiv2023

Essential Function of Membrane-Bound Transcription Factor MYRF in Promoting Transcription of miRNA lin-4 during C. elegans Development

Precise developmental timing control is essential for organism formation and function, but its mechanisms are unclear. In C. elegans, the microRNA lin-4 critically regulates developmental timing by post-transcriptionally downregulating the larval-stage-fate controller LIN-14. However, the mechanisms triggering the activation of lin-4 expression toward the end of the first larval stage remain unknown. We demonstrate that the transmembrane transcription factor MYRF-1 is necessary for lin-4 activation. MYRF-1 is initially localized on the cell membrane, and its increased cleavage and nuclear accumulation coincide with lin-4 expression timing. MYRF-1 regulates lin-4 expression cell-autonomously and hyperactive MYRF-1 can prematurely drive lin-4 expression in embryos and young first-stage larvae. The tandem lin-4 promoter DNA recruits MYRF-1GFP to form visible loci in the nucleus, suggesting that MYRF-1 directly binds to the lin-4 promoter. Our findings identify a crucial link in understanding developmental timing regulation and establish MYRF-1 as a key regulator of lin-4 expression.

developmental biology↗

bioRxiv2023

Acute stress reshapes third-party punishment and help decisions: Behavioral evidence and neurocomputational mechanisms

People tend to intervene in others injustices by either punishing the transgressor or helping the victim. Injustice events often occur under stressful circumstances. However, how acute stress affects a third partys intervention in injustice events remains open. Here, we show a stress-induced shift in third parties willingness to engage in help instead of punishment by acting on emotional salience and central-executive and theory-of-mind networks. Acute stress decreased the third partys willingness to punish the violator and the severity of the punishment and increased their willingness to help the victim. Computational modeling revealed a shift in intervention severity bias from punishment toward help under stress. This finding is consistent with the increased dorsolateral prefrontal engagement observed with higher amygdala activity and greater connectivity with the ventromedial prefrontal cortex. A brain connectivity theory-of-mind network predicted stress-induced severity bias in punishment. Our findings suggest a neurocomputational mechanism of how acute stress reshapes third parties decisions by reallocating neural resources in emotional, executive and mentalizing networks to inhibit punishment bias and decrease punishment severity.

neuroscience↗

bioRxiv2023

Identification of disulfidptosis-related-ferroptosis associated lncRNAs signature as a novel prognosis model for kidney renal clear cell carcinoma

Background: Clear cell renal cell carcinoma (ccRCC) represents 80% of all kidney cancers and has a poor prognosis. Newly discovered types of programmed cell death, ferroptosis and disulfidptosis, could have a direct impact on the outcome of KIRC cancer. Long non-coding RNAs (lncRNAs), which possess stable structures, can influence cancer prognosis and might be potential prognostic prediction factors for KIRC cancer. This study aims to investigate the correlation between disulfidptosis-related ferroptosis-related lncRNA and ccRCC in terms of immunity and prognosis. Methods: Coexpression analysis was employed to identify disulfidptosis-related ferroptosis-related long non-coding RNAs (DRFRLs). Differential expression analysis of DRFRLs was conducted using the limma package in R software, and the ConsensusClusterPlus package was utilized to identify molecular subtypes. Prognostic DRFRLs were identified via univariate Cox analysis, and a prognostic model based on eight DRFRLs was constructed through Cox regression analysis and the least absolute shrinkage and selection operator (LASSO) algorithm. Kaplan-Meier (K-M) survival curve analysis and receiver operating characteristic (ROC) curve analysis were utilized to evaluate the prognostic power of this model. Additionally, differences in biological function were investigated using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), while immunotherapy response was measured by utilizing tumor mutational burden (TMB) and tumor immune dysfunction and rejection (TIDE) scores. Single-cell analysis from the Tumor Immune Single Cell Center (TISCH) was employed to investigate cells with specific expression of the eight identified lncRNAs. Results: Two clusters (A and B) of disulfidptosis-related ferroptosis-related long non-coding RNAs (DRFRLs) were identified. Survival analysis revealed that patients with subtype A had a higher probability of survival compared to those in subtype B, suggesting that subtype A predicts better survival. An eight-lncRNA signature was established through LASSO-Cox regression, and Kaplan-Meier curves validated the accuracy of prognostic features prediction (P < 0.001). This signature demonstrated excellent prognostic performance, with an area under the curve (AUC) of 0.762, 0.761, and 0.749 at 1, 3, and 5 years in the training set and 0.790, 0.739, and 0.726 in the testing set, respectively. In the single-cell dataset, LINC01534, FOXD2-AS1, AC002070.1, and AL158212.3 were found to be expressed, with FOXD2-AS1 and AC002070.1 specifically expressing in the KC tumor immune microenvironment. Conclusions: The proposed signature of eight lncRNAs is a promising biomarker for predicting clinical outcomes and therapeutic responses in patients with ccRCC.

cancer biology↗

bioRxiv2023

Foveal RGCs develop abnormal calcium dynamics weeks after photoreceptor ablation

Objective or purposePhysiological changes in retinal ganglion cells (RGCs) have been reported in rodent models of photoreceptor (PR) loss but this has not been investigated in primates. By expressing both a calcium indicator (GCaMP6s) and an optogenetic actuator (ChrimsonR) in foveal RGCs of the macaque, we reactivated RGCs in vivo and assessed their response in the weeks and years following PR loss. DesignWe used an in vivo calcium imaging approach to record optogenetically evoked activity in deafferented RGCs in primate fovea. Cellular scale recordings were made longitudinally over a 10 week period following photoreceptor ablation and compared to responses from RGCs that had lost photoreceptor input more than two years prior. ParticipantsThree eyes received photoreceptor ablation, OD of a male Macaca mulatta (M1), OS of a female Macaca fascicularis (M2) and OD of a male Macaca fascicularis (M3). Two animals were used for in vivo recording, one for histological assessment. MethodsCones were ablated with an ultrafast laser delivered through an adaptive optics scanning light ophthalmoscope (AOSLO). A 0.5 s pulse of 25Hz 660nm light optogenetically stimulated RGCs, and the resulting GCaMP fluorescence signal was recorded using AOSLO. Measurements were repeated over 10 weeks immediately after PR ablation, at 2.3 years and in control RGCs. Main Outcome measuresThe calcium rise time, decay constant and sensitivity index of optogenetic mediated RGC were derived from GCaMP fluorescence recordings from 221 RGCs (Animal M1) and 218 RGCs (Animal M2) in vivo. ResultsFollowing photoreceptor ablation, the mean decay constant of the calcium response in RGCs decreased 1.5 fold (1.6{+/-}0.5 s to 0.6{+/-}0.3 s SD) over the 10 week observation period in subject 1 and 2.1 fold (2.5{+/-}0.5 s to 1.2{+/-}0.2 s SD) within 8 weeks in subject 2. Calcium rise time and sensitivity index were stable. Optogenetic reactivation remained possible 2.3 years after PR ablation. ConclusionsAltered calcium dynamics developed in primate foveal RGCs in the weeks after photoreceptor ablation. The mean decay constant of optogenetic mediated calcium responses decreased 1.5 - 2-fold. This is the first report of this phenomenon in primate retina and further work is required to understand the role these changes play in cell survival and activity.

physiology↗

bioRxiv2023

Estimating gross transcription rates from RNA level fluctuation data and the effects of sampling time intervals

Transcription rates are key biological parameters, but the estimation of transcription rates from RNA level fluctuation data by current methods is still problematic, considering in particular the derived relationship between RNA fragments from different samples and the neglect of the effects of sampling time intervals. Based on defining the gross transcription rate as the amount of converted complete nascent RNA divided by time, the present study developed an algorithm that calculated the cumulative transcription amount and RNA abundance at each time point by simulating moving windows to estimate gross transcription rates from RNA level fluctuation data and explore the effects of sampling time intervals on the estimation. The results showed that the gross transcription rates could be calculated from RNA level fluctuation data with the models fitting the experimental data well. In the analysis of 384 yeast genes, the genes with the highest gross transcription rates mainly played roles in cell division regulation and DNA replication, and the gene utilizing the most cellular resources for gene expression during the experiment was YNR016c, whose main functions are fatty acid biosynthesis and transporting proteins into the nucleus. The shapes of the RNA level curves affected the estimation of gross transcription rates, and the crests and valleys of the RNA level curves responded to higher gross transcription rates. Different scenarios of sampling time intervals could change the shapes of the RNA level curves, resulting in different estimation values of gross transcription rates. Given the potential applications of the present method, further improvements are expected.

bioinformatics↗

bioRxiv2023

Redefining Pleiotropic Drug Resistance in a Pathogenic Yeast: Pdr1 Functions as a Sensor of Cellular Stresses in Candida glabrata

Candida glabrata is a prominent opportunistic fungal pathogen of humans. The increasing incidence of C. glabrata infections is attributed to both innate and acquired resistance to antifungals. Previous studies suggest the transcription factor Pdr1 and several target genes encoding ABC transporters are critical elements of pleiotropic defense against azoles and other antifungals. This study utilizes Hermes transposon insertion profiling to investigate Pdr1-independent and Pdr1-dependent mechanisms that alter susceptibility to the frontline antifungal fluconazole. Several new genes were found to alter fluconazole susceptibility independent of Pdr1 (CYB5, SSK1, SSK2, HOG1, TRP1). A bZIP transcription repressor of mitochondrial function (CIN5) positively regulated Pdr1 while hundreds of genes encoding mitochondrial proteins were confirmed as negative regulators of Pdr1. The antibiotic oligomycin activated Pdr1 and antagonized fluconazole efficacy likely by interfering with mitochondrial processes in C. glabrata. Unexpectedly, disruption of many 60S ribosomal proteins also activated Pdr1, thus mimicking the effects of the mRNA translation inhibitors. Cycloheximide failed to fully activate Pdr1 in a cycloheximide-resistant Rpl28-Q38E mutant. Similarly, fluconazole failed to fully activate Pdr1 in a strain expressing a low-affinity variant of Erg11. Fluconazole activated Pdr1 with very slow kinetics that correlated with the delayed onset of cellular stress. These findings are inconsistent with the idea that Pdr1 directly senses xenobiotics and support an alternative hypothesis where Pdr1 senses cellular stresses that arise only after engagement of xenobiotics with their targets. ImportanceCandida glabrata is an opportunistic pathogenic yeast that causes discomfort and death. Its incidence has been increasing because of natural defenses to our common antifungal medications. This study explores the entire genome for impacts on resistance to fluconazole. We find several new and unexpected genes can impact susceptibility to fluconazole. Several antibiotics can also alter the efficacy of fluconazole. Most importantly, we find that Pdr1 - a key determinant of fluconazole resistance - is not regulated directly through binding of fluconazole and instead is regulated indirectly by sensing the cellular stresses caused by fluconazole blockage of sterol biosynthesis. This new understanding of drug resistance mechanisms could improve the outcomes of current antifungals and accelerate the development of novel therapeutics.

genetics↗

bioRxiv2023

Genomic epidemiology and multilevel genome typing of Bordetella pertussis

Bordetella pertussis is responsible for the respiratory infectious disease pertussis (or whooping cough), which causes one of the most severe diseases in infants, although it can be prevented by whole cell and acellular vaccines. The recent resurgence of pertussis is partially due to pathogen adaptation to vaccines as well as resistance to antimicrobials. Surveillance of current circulating and emerging strains is therefore vital to understand the risks they pose to public health. Although there is increased genomics based typing, a genomic nomenclature for this pathogen has not been well established. Here, we implemented the Multilevel Genome Typing (MGT) system for B. pertussis with five levels of resolution, which provide targeted typing of relevant lineages as well as discrimination of closely related strains at the finest scale. The low resolution levels can describe the distribution of alleles of major vaccine antigen genes such as ptxP, fim3, fhaB and prn as well as temporal and spatial trends within the B. pertussis global population. Mid-resolution levels enables typing of antibiotic resistant lineages and Prn deficient lineages within the ptxP3 clade. High resolution levels can capture small-scale epidemiology such as local transmission events and has comparable resolution to existing genomic methods of strain relatedness assessment. The scheme offers stable MGT type assignments aiding harmonisation of typing and communication between laboratories. The scheme is available at www.mgtdb.unsw.edu.au/pertussis/ is regularly updated from global data repositories and accepts public data submissions. The MGT scheme provides a comprehensive, robust, and scalable system for global surveillance of B. pertussis.

microbiology↗

bioRxiv2023

Artificial intelligence redefines RNA virus discovery

Current metagenomic tools can fail to identify highly divergent RNA viruses. We developed a deep learning algorithm, termed LucaProt, to discover highly divergent RNA-dependent RNA polymerase (RdRP) sequences in 10,487 metatranscriptomes generated from diverse global ecosystems. LucaProt integrates both sequence and predicted structural information, enabling the accurate detection of RdRP sequences. Using this approach we identified 161,979 potential RNA virus species and 180 RNA virus supergroups, including many previously poorly studied groups, as well as RNA virus genomes of exceptional length (up to 47,250 nucleotides) and genomic complexity. A subset of these novel RNA viruses were confirmed by RT-PCR and RNA/DNA sequencing. Newly discovered RNA viruses were present in diverse environments, including air, hot springs and hydrothermal vents, and both virus diversity and abundance varied substantially among ecosystems. This study advances virus discovery, highlights the scale of the virosphere, and provides computational tools to better document the global RNA virome. In briefA deep learning algorithm (LucaProt) that integrates both sequence and predicted structural information was employed to identify highly divergent RNA viral "dark matter" in 10,487 metatranscriptomes from diverse global ecosystems. A total of 161,979 potential RNA virus species and 180 RNA virus supergroups was unveiled using this AI approach, including many understudied groups.

microbiology↗

bioRxiv2023

EGFR+ lung adenocarcinomas coopt alveolar macrophage metabolism and function to support EGFR signaling and growth

The limited efficacy of currently approved immunotherapies in EGFR-mutant lung adenocarcinoma (LUAD) underscores the need to better understand mechanisms governing local immunosuppression. Elevated surfactant and GM-CSF secretion from the transformed epithelium induces tumor-associated alveolar macrophages (TA-AM) to proliferate and support tumor growth by rewiring inflammatory functions and lipid metabolism. TA-AM properties are driven by increased GM-CSF--PPAR{gamma} signaling and inhibition of airway GM-CSF or PPAR{gamma} in TA-AMs suppresses cholesterol efflux to tumor cells, which impairs EGFR phosphorylation and restrains LUAD progression. In the absence of TA-AM metabolic support, LUAD cells compensate by increasing cholesterol synthesis, and blocking PPAR{gamma} in TA-AMs simultaneous with statin therapy further suppresses tumor progression and increases T cell effector functions. These results reveal new therapeutic combinations for immunotherapy resistant EGFR-mutant LUADs and demonstrate how such cancer cells can metabolically co-opt TA-AMs through GM-CSF--PPAR{gamma} signaling to provide nutrients that promote oncogenic signaling and growth.

immunology↗

bioRxiv2023

Artificial selection footprints in domestic chicken genomes

Accurate and low-cost next generation sequencing technologies make re-sequencing of large populations of a species possible. Although many studies related to artificial selection signatures of commercial and indigenous chickens have been carried out, quite a small number of genes have been found to be under selection. In this study, we re-sequenced 85 individuals of five indigenous chicken breeds with distinct traits from Yunnan, a southwest province of China. By analyzing these indigenous chickens together with 116 individuals of commercial chickens (broilers and layers) and 35 individuals of red jungle fowl, we find a substantially large number of selective sweeps and affected genes for each chicken breed using a rigorous statistic model than previously reported. We confirm most of previously identified selective sweeps and affected genes. Meanwhile the vast majority ([~]98.3%) of our identified selective sweeps overlap known chicken quantitative trait loci. Thus, our predictions are highly reliable. For each breed, we also identify candidate genes and selective sweeps that might be related to the unique traits of the chickens.

bioinformatics↗

bioRxiv2023

Molecular understanding of anthocyanin biosynthesis activated by PAP1 in engineered red Artemisia annua cells and regulation of 2, 4-dichlorophenoxyacetic acid

Artemisia annua is an effective antimalarial medicinal crop. We have established anthocyanin-producing red cell cultures from this plant with the overexpression of Production of Anthocyanin Pigment 1 (PAP1) encoding a R2R3MYB transcription factor. To understand the molecular mechanism by which PAP1 activated the entire anthocyanin pathway, we mined the genomic sequences of A. annua and obtained eight promoters of the anthocyanin pathway genes. Sequence analysis identified four types of AC cis-elements from six promoters, the MYB response elements (MRE) bound by PAP1. In addition, six promoters were determined to have at least one G-Box cis-element. Eight promoters were cloned for activity analysis. Duel luciferase assays showed that PAP1 significantly enhanced the promoting activity of seven promoters, indicating that PAP1 turned on the biosynthesis of anthocyanins via the activation of these pathway gene expression. To understand how 2,4-dichlorophenoxyacetic acid (2,4-D), an auxin, regulates the PAP1-activated anthocyanin biosynthesis, five different concentrations (0, 0.05, 0.5, 2.5, and 5 M) were tested to characterize anthocyanin production and profiles. The resulting data showed that the concentrations tested decreased the fresh weight of callus growth, anthocyanin levels, and the production of anthocyanins per petri dish. HPLC-qTOF-MS/MS based profiling showed that these concentrations did not alter anthocyanin profiles. Real time RT-PCR was completed to characterize the expression PAP1 and four representative pathway genes. The results showed that the five concentrations reduced the expression levels of the constitutive PAP1 transgene and three pathway genes significantly and eliminated chalcone synthase gene in expression either significantly or slightly. These data indicate that the constitutive PAP1 expression depends on gradients added in the medium. Based on these findings, the regulation of 2,4-D is discussed for anthocyanin engineering in red cells of A. annua. ConclusionPromoters of eight anthocyanin pathway genes were cloned. Four types of AC cis-elements were identified from six promoters and G-Box elements were also determined from six promoters. PAP1 enhanced the activity of eight promoters. 2,4-D downregulated the expression of the constitutive PAP1 transgene leading to the decrease the biosynthesis of anthocyanins.

plant biology↗

bioRxiv2023

HBV rewires liver cancer signaling by altering PP2A complexes

Infection by hepatitis B virus (HBV) increases risk for liver cancer by inducing inflammation, cellular stress and cell death. To elucidate the molecular pathways by which HBV promotes cancer development and progression, we used affinity purification mass spectrometry to comprehensively map a network of 145 physical interactions between HBV and human host proteins in hepatocellular carcinoma (HCC). We find that viral proteins target host factors that are preferentially mutated in non-HBV-associated HCC, implicating cancer pathways whose interaction with HBV plays a role in HCC. Focusing on proteins that directly interact with the HBV oncoprotein X (HBx), we show that HBx remodels the PP2A phosphatase complex, altering its effect on tumor signaling. HBx excludes striatin-family regulatory subunits from PP2A, causing Hippo kinase activation and unmasking a requirement for mTOR complex 2 to maintain expression of the YAP oncoprotein in HCC. Thus, HBV rewires HCC to expose potentially targetable signaling dependencies. SignificancePrecision medicine has revolutionized cancer treatment but remains elusive for HCC. We used proteomics to define HBV/host interactions and integrated them with HCC mutations. The results implicate modifiers of HCC behavior via remodeling of host complexes and illuminate new biological mechanisms in advanced disease for therapeutic investigation.

cancer biology↗

bioRxiv2023

PIF4 promotes water use efficiency during fluctuating light and drought resistance in rice

Molecular mechanism of intrinsic water use efficiency (iWUE) during fluctuating light (FL) was rarely understood. In this study, we investigated five parameters of iWUE under FL in 200 Minicore rice accessions. Among them, a novel trait, WUEFL (averaged iWUE during FL) has highest SNP heritability in these parameters. GWAS identifies six candidate genes, and PIF4 is highly expressed in high iWUEFL rice subgroup. Nine SNPs were significantly associated with iWUEFL, and v3 SNP located at -1,075 bp of PIF4 promoter shows highest sensitives to light. Deletion of v3 in a rice cultivar, WYG7 (PIF4v3m) leads to [~]20% reduction in iWUEFL, and overexpressing PIF4 causes 25% increase in iWUEFL under DS. There are 85% reduction in adenosine 3,5-diphosphate (PAP) amounts together with 73% increase in SAL1 gene abundance in PIF4v3m than WYG7. PIF4 transcriptionally repress and activate SAL1 and NHX1, respectively, through binding to G-box motifs of the two genes, which leads to 16% reduction and 5% increase in iWUEFL in co-overexpression rice lines of PIF4-SAL1 and PIF4-NHX1, respectively, relative to PIF4-OE under DS. We proposed that PIF4 promotes iWUEFL and stomatal adjustment via targeting the G-box motif of SAL1 and NHX1 genes during FL, eventually facilitating to drought resistance.

plant biology↗

bioRxiv2023

Speeding up interval estimation for R2-based mediation effect of high-dimensional mediators via cross-fitting

Mediation analysis is a useful tool in investigating how molecular phenotypes such as gene expression mediate the effect of exposure on health outcomes. However, commonly used mean-based total mediation effect measures may suffer from cancellation of component-wise mediation effects in opposite directions in the presence of high-dimensional omics mediators. To overcome this limitation, we recently proposed a variance-based R-squared total mediation effect measure that relies on the computationally intensive nonparametric bootstrap for confidence interval estimation. In the work described herein, we formulated a more efficient two-stage, cross-fitted estimation procedure for the R2 measure. To avoid potential bias, we performed iterative Sure Independence Screening (iSIS) in two subsamples to exclude the non-mediators, followed by ordinary least squares regressions for the variance estimation. We then constructed confidence intervals based on the newly derived closed-form asymptotic distribution of the R2 measure. Extensive simulation studies demonstrated that this proposed procedure is much more computationally efficient than the resampling-based method, with comparable coverage probability. Furthermore, when applied to the Framingham Heart Study, the proposed method replicated the established finding of gene expression mediating age-related variation in systolic blood pressure and identified the role of gene expression profiles in the relationship between sex and high-density lipoprotein cholesterol level. The proposed estimation procedure is implemented in R package CFR2M.

molecular biology↗

bioRxiv2023

An ULK1/2-PXN mechanotransduction complex suppresses breast cancer cell migration

The remodeling and stiffening of the extracellular matrix (ECM) associated with breast cancers is a well-recognized modulator of disease progression. However, how changes in the mechanical properties of the ECM are converted into biochemical signals that direct tumor cell migration and metastasis remains poorly characterized. Here, we describe a new role for the autophagy-inducing serine/threonine kinases ULK1 and ULK2 in mechanotransduction. We demonstrate that ULK1/2 activity inhibits the assembly of actin stress fibers and focal adhesions (FAs), and as a consequence impedes cell contraction and migration. Mechanistically, we identify PXN/paxillin, a key component of the mechanotransducing machinery, as a direct binding partner and substrate of ULK1/2. ULK-mediated phosphorylation of PXN at S32 and S119 weakens homotypic interactions and liquid-liquid phase separation of PXN, impairing FA assembly, which in turn impedes the mechanotransduction of breast cancer cells. ULK1/2 and the well characterized PXN regulator, FAK/Src, have opposing functions on mechanotransduction and compete for phosphorylation of adjacent serine and tyrosine residues. Thus, our study reveals ULK1/2 as important regulators of PXN-dependent mechanotransduction. HighlightsO_LIULK1/2 interact with PXN and phosphorylate PXN at S32 and S119 in response to mechanical stimuli C_LIO_LIULK1/2-mediated phosphorylation of PXN regulates mechanotransduction and migration of breast cancer cells C_LIO_LIULK1/2 modulate the biomaterial properties of focal adhesions through PXN phosphorylation C_LIO_LIULK1/2 and FAK/Src act antagonistically in mechanotransduction through competitive phosphorylation of PXN C_LI

cell biology↗