Biology subjects

Fu, X.

Publications and source records attributed to Fu, X..

At least 181 records · Page 10Linked to original sources

bioRxiv2020

Saccharomyces cerevisiae Ecm2 Modulates the Catalytic Steps of pre-mRNA Splicing

Genetic, biochemical, and structural studies have elucidated the molecular basis for spliceosome catalysis. Splicing is RNA catalyzed and the essential snRNA and protein factors are well-conserved. However, little is known about how non-essential components of the spliceosome contribute to the reaction and modulate the activities of the fundamental core machinery. Ecm2 is a non-essential yeast splicing factor that is a member of the Prp19-related complex of proteins. Cryo-electron microscopy (cryo-EM) structures have revealed that Ecm2 binds the U6 snRNA and is entangled with Cwc2, another non-essential factor that promotes a catalytically active conformation of the spliceosome. These structures also indicate that Ecm2 and the U2 snRNA likely form a transient interaction during 5 splice site (SS) cleavage. We have characterized genetic interactions between ECM2 and alleles of splicing factors that alter the catalytic steps in splicing. In addition, we have studied how loss of ECM2 impacts splicing of pre-mRNAs containing non-consensus or competing SS. Our results show that ECM2 functions during the catalytic stages of splicing. It facilitates the formation and stabilization of the 1st-step catalytic site, promotes 2nd-step catalysis, and permits alternate 5 SS usage. We propose that Cwc2 and Ecm2 can each fine-tune the spliceosome active site in unique ways. Their interaction network may act as a conduit through which splicing of certain pre-mRNAs, such as those containing weak or alternate splice sites, can be regulated.

biochemistry↗

bioRxiv2020

Age-related Changes in Diffuse Optical Tomography Sensitivity to the Cortex in Infancy

SignificanceDiffuse optical tomography (DOT) uses near-infrared light spectroscopy (NIRS) to measure changes in cerebral hemoglobin concentration. Anatomical interpretations of NIRS data requires accurate descriptions of the cranio-cerebral relations and DOT sensitivity to the underlying cortical structures. Such information is limited for pediatric populations because they undergo rapid head and brain development. AimThe present study aimed to investigate age-related differences in scalp-to-cortex distance and mapping between scalp locations and cortical regions of interest (ROIs) among infants (2 weeks to 24 months with narrow age bins), children (4 and 12 years) and adults (20 to 24 years). ApproachWe used spatial scalp projection and photon propagation simulation methods with age-matched realistic head models based on MRIs. ResultsThere were age-group differences in the scalp-to-cortex distances in infancy. The developmental increase was magnified in children and adults. There were systematic age-related differences in the probabilistic mappings between scalp locations and cortical ROIs. ConclusionsOur findings have important implications in the design of sensor placement and making anatomical interpretations in NIRS and fNIRS research. Age-appropriate realistic head models should be used to provide anatomical guidance for standalone DOT data in infants.

neuroscience↗

bioRxiv2020

Transposable Element-Gene Splicing Modulates the Transcriptional Landscape of Human Pluripotent Stem Cells

Transposable elements (TEs) occupy nearly 50% of mammalian genomes and are both potential dangers to genome stability and functional genetic elements. TEs can be expressed and exonised as part of a transcript, however, their full contribution to the transcript splicing remains unresolved. Here, guided by long and short read sequencing of RNAs, we show that 26% of coding and 65% of non-coding transcripts of human pluripotent stem cells (hPSCs) contain TEs. Different TE families have unique integration patterns with diverse consequences on RNA expression and function. We identify hPSC-specific splicing of endogenous retroviruses (ERVs) as well as LINE L1 elements into protein coding genes that generate TE-derived peptides. Finally, single cell RNA-seq reveals that proliferating hPSCs are dominated by ERV-containing transcripts, and subpopulations express SINE or LINE-containing transcripts. Overall, we demonstrate that TE splicing modulates the pluripotency transcriptome by enhancing and impairing transcript expression and generating novel transcripts and peptides.

genomics↗

bioRxiv2020

Genome-wide association study of flowering time reveals complex genetic heterogeneity and epistatic interactions in rice

Since domestication, rice has cultivated in a wide range of latitudes with different day lengths. Selection of diverse natural variations in heading date and photoperiod sensitivity is critical for adaptation of rice to different geographical environments. To unravel the genetic architecture underlying natural variation of rice flowering time, we conducted a genome wide association study (GWAS) using several association analysis strategies with a diverse worldwide collection of 529 O. sativa accessions. Heading date was investigated in three environments under long-day or short-day conditions, and photosensitivity was evaluated. By dividing the whole association panel into subpopulations and performing GWAS with both linear mixed models and multi-locus mixed-models, we revealed hundreds of significant loci harboring novel candidate genes as well as most of the known flowering time genes. In total, 127 hotspots were detected in at least two GWAS. Universal genetic heterogeneity was found across subpopulations. We further detected abundant interactions between GWAS loci, especially in indica. Functional gene families were revealed from enrichment analysis of the 127 hotspots. The results demonstrated a rich of genetic interactions in rice flowering time genes and such epistatic interactions contributed to the large portions of missing heritability in GWAS. It suggests the increased complexity of genetic heterogeneity might discount the power of increasing the sample sizes in GWAS.

genetics↗

bioRxiv2020

Parabrachial neuron types categorically encode thermoregulation variables during heat defense

Heat defense is crucial for survival and fitness, and its dysregulation may result in deaths due to poor management. Transmission of thermosensory signals into hypothalamic thermoregulation centers represent a key layer of regulation in heat defense. However, the mechanism by which these signals are transmitted into the hypothalamus remains poorly understood. Here, we reveal that glutamatergic prodynorphin and cholecystokinin neuron populations in the lateral parabrachial (LPB) are progressively recruited to defend elevated body temperature. These two nonoverlapping neuron types form circuitries with downstream preoptic hypothalamic neurons to inhibit BAT thermogenesis and activate tail vasodilation, respectively. Both circuitries are selectively activated by warm temperatures and are required for fever limiting. The prodynorphin circuitry is further required for regulation of energy expenditure and weight homeostasis. Thus, these findings establish that the genetic and functional specificity of heat defense neurons occurs as early as in the LPB and uncover categorical neuron types for encoding two heat defense variables, which may provide targets for treating thermoregulation disorders.

neuroscience↗

bioRxiv2020

Assembly intermediates of orthoreovirus captured in the cell

Traditionally molecular assembly pathways for viruses have been inferred from high resolution structures of stable intermediates purified in vitro, and from low resolution images of cell sections as well as from genetic approaches including conditionally lethal mutants. Here, we directly visualise a previously unsuspected single shelled icosahedral intermediate for a mammalian orthoreovirus, in addition to the expected virions, in cryo-preserved infected cells by cryo-electron tomography of cellular lamellae1,2. Particle classification and averaging yielded structures at resolutions as high as 5.6 [A], sufficient to identify secondary structural elements and place known molecular structures, allowing us to produce an atomic model of the intermediate, comprising 120 copies of protein {lambda}1 and 120 copies of {sigma}2. This {lambda}1 shell is in a collapsed form compared to the mature virions, with the molecules pushed inwards at the icosahedral 5-folds by ~100 [A]. This grossly indented shell, although produced by a mammalian reovirus, is reminiscent of the first assembly intermediate of prokaryotic dsRNA viruses belonging to a different virus family3, adding weight to the supposition that these diverse viruses share a common ancestor, and suggesting mechanisms for the assembly of viruses of the Reoviridae. Such methodology holds enormous promise for the dissection of the replication cycle of many viruses.

microbiology↗

bioRxiv2020

Serial cryoFIB/SEM reveals profound cytoarchitectural disruptions caused by a pathogenic mutation in Leigh syndrome patient cells

The advancement of serial cryo-FIB/SEM offers a new opportunity to study large volumes of near-native, fully hydrated frozen cells and tissues at voxel sizes of 10 nm and below. We explored this capability for pathologic characterization of vitrified human patient cells. We demonstrate profound disruption of subcellular architecture in primary fibroblasts from a Leigh syndrome patient harboring a disease-causing mutation in USMG5 protein responsible for impaired mitochondrial energy production.

biophysics↗

bioRxiv2020

Genetic inactivation of the translin/trax microRNA-degrading enzyme phenocopies the robust adiposity induced by Translin (Tsn) deletion

ObjectiveDeletion of Translin (Tsn) from mice induces an unusual metabolic profile characterized by robust adiposity, normal body weight and glucose tolerance. Translin (TN) protein and its partner, trax (TX), form the TN/TX microRNA-degrading enzyme. Since the microRNA system plays a prominent role in regulating metabolism, we reasoned that the metabolic profile displayed by Tsn KO mice might reflect dysregulation of microRNA signaling. MethodsTo test this hypothesis, we inserted a mutation, E126A, in Tsnax, the gene encoding TX, that abolishes the microRNA-degrading enzymatic activity of the TN/TX complex. In addition, to help define the cell types that drive the adiposity phenotype, we have also generated mice with floxed alleles of Tsn or Tsnax. ResultsIntroduction of the E126A mutation in Tsnax does not impair expression of TN or TX proteins or their co-precipitation. Furthermore, these mice display selective increases in microRNAs that match those induced by Tsn deletion, confirming that this mutation in Tsnax inactivates the microRNA-degrading activity of the TN/TX complex. Mice homozygous for the Tsnax (E126A) mutation display a metabolic profile that closely mimics that of Tsn KO mice. Selective deletion of Tsn or Tsnax from either adipocytes or hepatocytes, two candidate cell types, does not phenocopy the elevated adiposity displayed by mice with constitutive Tsn deletion or the Tsnax(E126A) mutation. Furthermore, global, conditional deletion of Tsn in adulthood does not elicit increased adiposity. ConclusionTaken together, these findings indicate that inactivation of the TN/TX microRNA-degrading enzyme during development is necessary to drive the robust adiposity displayed by Tsn KO mice.

cell biology↗

bioRxiv2020

Visual function restoration in genetically blind mice via endogenous cellular reprogramming

In this study, we developed an in-situ cellular reprogramming strategy for potent restoration of vision in advanced/end-stage retinitis pigmentosa (RP). Via repressing PTB, an RNA binding protein critical for converting non-neuronal cells to the neuronal lineage, we successfully reprogramed Muller glia to a retinal neuronal fate, and then to cones. We demonstrated that this cellular reprogramming approach was able to rescue retinal photoreceptor degeneration and restore visual functions in two RP mouse models with total blindness, suggesting a novel universal strategy for treating end-stage degenerative diseases.

cell biology↗

bioRxiv2020

MiR-203 inhibits the proliferation, invasion, and migration of pancreatic cancer cells by down-regulating fibroblast growth factor 2

BackgroundAberrant fibroblast growth factor 2 (FGF2) expression is a major cause of poor prognosis in pancreatic cancer. MiR-203 is a newly discovered microRNA (miRNA) that can affect the biological behavior of tumors. This study investigated whether miR-203 can regulate FGF2 expression and its role in pancreatic cancer cell proliferation, apoptosis, invasion, and migration. MethodsMiR-203 expression in different cell lines was examined by qRT-PCR, followed by the establishment of knockdown and overexpression cell models. We used the CCK-8 assay to examine cell proliferation and the annexin V-APC/7-AAD double-staining method to detect apoptosis. In addition, we used wound healing and transwell assays to investigate the effects of miR-203 on the migration and invasion of pancreatic cancer cells. The effects of miR-203 knockdown and overexpression on FGF2 mRNA expression were detected by qRT-PCR. We also overexpressed FGF2 and examined the effects of FGF2 overexpression on the proliferation, apoptosis, invasion, and migration of pancreatic cancer cells. The binding of miR-203 to FGF2 was assessed by a luciferase reporter assay. ResultsWe found that the miR-203 expression level was significantly down-regulated in pancreatic cancer cells compared to normal pancreatic cells. Functionally, the knockdown of miR-203 inhibited cell proliferation and increased apoptosis. Equally important, miR-203 reduced the migration and invasion of pancreatic cancer cells. In addition, we found that miR-203 overexpression inhibited FGF2 expression in pancreatic cancer cells by qRT-PCR. FGF2 overexpression significantly affected the proliferation, invasion, and metastasis of pancreatic cancer cells. Mechanistically, miR-203 base-paired with the FGF2 mRNA, resulting in the knockdown of the FGF2 mRNA and the down-regulation of the FGF2 protein. ConclusionsMiR-203 inhibits FGF2 expression, regulates the proliferation of pancreatic cancer cells, and inhibits the invasion and metastasis of pancreatic cancer cells.

cancer biology↗

bioRxiv2020

An Experimental Validation of the Computer Fluid Dynamics of Normal Human Nasal Airflow Using a Precise 3-D Printing Model

Computer Fluid Dynamics (CFD) is a popular method for studying airflow of nasal cavities. However, the data of CFD studies has rarely been validated through experiments. To test the accuracy of CFD computation, we studied the consistency of the air pressure of nasal cavities in the CFD and the experiment. A proportional resin model of a normal human subjects nasal cavities was created by a 3-d printer with a precision value of 0.1mm. The pressure of 63 check points in the nasal cavities in different breathing states was measured. The experimental data was compared with the data obtained by CFD simulation. At the flow rates of 180 ml s-1 and 560 ml s-1, the pressure in all check points remained highly consistent with the CFD data. At 1100 ml s-1 flow rate, there was a significant deviation in the posterior segment of the nasal cavity during exhalation. The method used in this study to measure the pressure in the nasal cavities can be used in experimental validation of CFD data. The computational methods and the boundary conditions used in this study resulted in a high agreement between the results of the CFD simulation and the experiment. Author SummaryIn the contemporary era, Computer fluid dynamics (CFD) is the mainstream method for studying air flow. Due to the complex anatomical structure of the nasal cavity, the CFD results of the nasal flow have rarely been experimentally verified. This study provides a method to verify the methods and results of nasal CFD. We printed an accurate model of a normal persons nasal cavity with a high-precision 3D printer. In this nasal cavity model, we set 63 small holes to detect the air pressure of the places we concerned. Three different nasal flow quantity are used to represent different breathing conditions: high (1100 ml s-1), medium (560 ml s-1), and low (180 ml s-1). In medium and low nasal flow quantities, our CFD results are in good agreement with the experimental pressure values. On this basis, we analyzed the characteristics of nasal airflow in normal people. The method used in this study to measure the pressure in the nasal cavities can be used in experimental measurements of the partial resistance of the nasal cavity. With proper modification, it can be applied to the clinical practice for nasal resistance, giving more help for the design of the operation plan.

biophysics↗

bioRxiv2020

Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data

Computational reconstruction of clonal evolution in cancers has become a crucial tool for understanding how tumors initiate and progress and how this process varies across patients. The field still struggles, however, with special challenges of applying phylogenetic methods to cancers, such as the prevalence and importance of copy number alteration (CNA) and structural variation (SV) events in tumor evolution, which are difficult to profile accurately by prevailing sequencing methods in such a way that subsequent reconstruction by phylogenetic inference algorithms is accurate. In the present work, we develop computational methods to combine sequencing with multiplex interphase fluorescence in situ hybridization (miFISH) to exploit the complementary advantages of each technology in inferring accurate models of clonal CNA evolution accounting for both focal changes and aneuploidy at whole-genome scales. We demonstrate on simulated data that incorporation of FISH data substantially improves accurate inference of focal CNA and ploidy changes in clonal evolution from deconvolving bulk sequence data. Analysis of real glioblastoma data for which FISH, bulk sequence, and single cell sequence are all available confirms the power of FISH to enhance accurate reconstruction of clonal copy number evolution in conjunction with bulk and optionally single-cell sequence data. Availabilitygithub.com/CMUSchwartzLab/FISH_deconvolution Contactrussells@andrew.cmu.edu

bioinformatics↗

bioRxiv2020

Exploiting evolutionary trade-offs to combat antibiotic resistance

Antibiotic resistance frequently evolves through fitness trade-offs in which the genetic alterations that confer resistance to a drug can also cause growth defects in resistant cells. Here, through experimental evolution in a microfluidics-based turbidostat, we demonstrate that antibiotic-resistant cells can be efficiently inhibited by amplifying the fitness costs associated with drug-resistance evolution. Using tavaborole-resistant E. coli as a model, we show that genetic mutations in leucyl-tRNA synthetase (that underlie tavaborole resistance) make resistant cells intolerant to norvaline, a chemical analog of leucine that is mistakenly used by tavaborole-resistant cells for protein synthesis. We then show that tavaborole-sensitive cells quickly outcompete tavaborole-resistant cells in the presence of norvaline due to the amplified cost of the molecular defect of tavaborole resistance. This finding illustrates a potentially generalizable approach for combating therapeutic resistance, prolonging the effectiveness of drugs and enabling the use of drugs that are no longer effective due to the rapid evolution of resistance.

evolutionary biology↗

bioRxiv2020

Derived ecological niches of indoor microbes are crucial for asthma symptoms in university dormitories

Increasing evidences from home environment indicate that microbiome community is associated with asthma. However, indoor microbiome composition can be highly diverse and dynamic, and thus current studies fail to produce consistent association. Chinese university dormitories are special high-density dwellings with a standard built environment and personal characteristics for occupants, which can be used to disentangle the complex interactions between microbes, environmental characteristics and asthma. Settled air dust and floor dust was collected from 87 dormitory rooms in Shanxi University. Bacterial community was characterized by 16S rRNA amplicon sequencing. Students (n = 357) were surveyed for asthma symptoms. Asthma symptoms were not associated with the overall bacterial richness, but associated with different phylogenetic classes. Taxa richness and abundance in Clostridia and Bacteroidia were positively associated with asthma (p < 0.05), and these taxa were mainly derived from human gut. Taxa richness (p < 0.1) and abundance (p < 0.05) in Alphaproteobacteria and Actinobacteria were protectively associated with asthma, and these taxa were mainly derived from outdoor environment. Building age, floor and curtain cleaning frequency shaped the overall bacterial community of air dust (p < 0.05). Frequent curtain cleaning increased the relative abundance of 10 protective genera (p < 0.05), and old buildings had mix effects to protective genera (p < 0.05). Our data shows that taxa from different phylogenetic classes and ecological niches have different health effects, indicating the importance of incorporating evolutionary and ecological concepts in revealing general patterns in the microbiome asthma association analysis.

microbiology↗

bioRxiv2020

Acute Stress Desensitizes Hypothalamic CRH Neurons to Norepinephrine and Physiological Stress

Noradrenergic afferents to corticotropin releasing hormone (CRH) neurons of the hypothalamic paraventricular nucleus (PVN) provide a major excitatory drive to the hypothalamic-pituitary-adrenal (HPA) axis via 1 adrenoreceptor activation. The ascending noradrenergic afferents are recruited preferentially by physiological, rather than psychological, stress modalities. Glucocorticoids secreted in response to HPA activation feed back onto the hypothalamus to negatively regulate the HPA axis, providing a critical autoregulatory constraint that prevents glucocorticoid overexposure. Whether differential negative feedback mechanisms target stress modality-specific HPA activation is not known. Here, we reveal a desensitization of the 1 adrenoreceptor activation of the HPA axis following acute stress that is mediated by rapid glucocorticoid regulation of adrenoreceptor trafficking. Prior stress desensitized the HPA axis to subsequent physiological, but not psychological, stress. Our findings demonstrate rapid glucocorticoid suppression of adrenoreceptor signaling in CRH neurons that is specific to physiological stress activation, and reveal, therefore, a rapid, modality-selective glucocorticoid feedback mechanism.

neuroscience↗

bioRxiv2019

Distinct microbiome composition of floor and air dust distort richness estimation in university dormitories

The number of culture-independent indoor microbiome study has increased remarkably in recent years, but microbial composition among different sampling strategies remains poorly characterized and their impact to downstream microbiome analysis is also not clear. In this study, we reported a case study of microbial composition of floor and air dust in 87 dormitory rooms of Shanxi University, China. Floor and air dust were collected by vacuum cleaner and petri-dish, respectively, and the bacterial composition was characterized by 16S rRNA sequencing. The composition of floor and air dust differed significantly (R2 = 0.65, p < 0.001, Adonis), and Pseudomonas dominated in floor dust (75.1%) but was less common in air dust (1.9%). The top genera in air dust, including Ralstonia (15.6%), Pelomonas (11.3%), Anoxybacillus (9.3%) and Ochrobactrum (6.2%), all accounted for < 1% abundance in floor dust. The dominant Pseudomonas in floor dust swamped low frequency organisms, leading to significant lower number of operational taxonomic units (OTUs) compared with air dust in the same sequencing depth. The different microbial composition of floor and air dust can lead to differences in downstream bioinformatics analyses. We searched the dormitory microbiome against ~200,000 samples deposited in Microbiome Search Engine (MSE), and found that the compositions of floor dust samples were similar to samples from building environment and human nasopharynx, whereas the compositions of the air dust samples were similar to mosquito tissues. ImportanceIncreasing number of indoor microbiome studies has been conducted in recent years, but the impact of sampling strategy is far from clear. In this study, we reported that the floor and air sampling can lead to drastic variation in microbial composition and downstream analyses in university dormitories, including microbial diversity estimation and compositional similarity search. Thus, the bioinformatics analysis results need to be interpreted with caution in microbiome studies, and it may be necessary to collected samples from different sampling strategies to comprehensively characterize the microbial composition and exposure to human occupants in an indoor environment.

microbiology↗

bioRxiv2019

Continental-scale microbiome study reveals different environmental characteristics determining microbial richness and composition/quantity in hotel rooms

Culture-independent microbiome surveys have been conducted in homes, hospitals, schools, kindergartens and vehicles for public transport, revealing diverse microbial distributions in built environments. However, microbiome surveys have not been conducted in hotel environments; thus, the composition and associated environmental factors are not clear. We presented the first continental-scale microbiome study of hotel rooms (n = 68) spanning large geographic regions. Bacterial and fungal communities were described by amplicon sequencing of the 16S rRNA gene and internal transcribed spacer (ITS) region and quantitative PCR. Similar numbers of bacterial (4,344) and fungal (4,555) operational taxonomic units were identified, but fungal taxa showed a local distribution compared with bacterial taxa. Aerobic, ubiquitous bacteria dominated the hotel microbiome with high compositional similarity to previous samples from building and human nasopharynx environments. The abundance of Aspergillus was negatively correlated with latitude and accounted for [~]80% of the total fungal load in seven low-latitude hotels. We calculated the association between hotel microbial dynamics and 16 indoor and outdoor environmental characteristics. Fungal {beta}-diversity and quantity showed concordant variation and were associated with the same environmental characteristics, including latitude, quality of the interior, proximity to the sea and visible mold, while -diversity decreased with heavy traffic (95% CI: -127.05 to -0.25) and wall-to-wall carpet (95% CI: -47.60 to -3.82). Bacterial {beta}-diversity was associated with latitude, quality of the interior and floor type, while -diversity decreased with recent decoration (95% CI -179.00 to -44.55) and mechanical ventilation (95% CI: -136.71 to -5.12). ImportanceThis is the first microbiome study to characterize microbial composition and associated environmental characteristics. In this study, we found concordant variation between microbial {beta}-diversity and absolute quantity and discordant variation between {beta}-diversity/quantity and -diversity. Our study can be used to promote hotel hygiene standards and provide resource information for future microbiome and exposure studies associated with health effects in hotel rooms.

microbiology↗

bioRxiv2019

The microRNA476a/RFL module regulates adventitious root formation through a mitochondria-dependent pathway in Populus

Adventitious root (AR) formation at the base of stem cuttings determines the efficiency of clonal propagation for woody plants. Many endogenous and environmental factors influence AR formation. However, our knowledge about the regulation of AR development by mitochondrial metabolism in plants is very limited. Here we identified Populus-specific miR476a as a novel regulator of wound-induced adventitious rooting via orchestrating mitochondrial homeostasis in poplar. MiR476a exhibited inducible expression during AR formation and directly targets several Restorer of Fertility like (RFL) genes encoding mitochondrion-localized pentatricopeptide repeat proteins. Genetic modification of miR476-RFL expression revealed the miR476/RFL-mediated dynamic regulation of mitochondrial homeostasis on AR formation in transgenic poplar. Furthermore, mitochondrial perturbation via exogenous chemical inhibitor validated that the miR476a/RFL-directed AR formation depended on mitochondrial regulation though modulating the auxin pathway. Our results established a miRNA-directed mitochondrion-auxin signaling cascade required for AR development, providing novel insights into the understanding of mitochondrial regulation on plant developmental plasticity.

plant biology↗