Biology subjects

Pan, Y.

Publications and source records attributed to Pan, Y..

At least 217 records · Page 12Linked to original sources

bioRxiv2021

PHARP: A pig haplotype reference panel for genotype imputation

Pigs not only function as a major meat source worldwide but also are commonly used as an animal model for studying human complex traits. A large haplotype reference panel has been used to facilitate efficient phasing and imputation of relatively sparse genome-wide microarray chips and low-coverage sequencing data. Using the imputed genotypes in the downstream analysis, such as GWASs, TWASs, eQTL mapping and genomic prediction (GS), is beneficial for obtaining novel findings. However, currently, there is still a lack of publicly available and high-quality pig reference panels with large sample sizes and high diversity, which greatly limits the application of genotype imputation in pigs. In response, we built the pig Haplotype Reference Panel (PHARP) database. PHARP provides a reference panel of 2,012 pig haplotypes at 34 million SNPs constructed using whole-genome sequence data from more than 49 studies of 71 pig breeds. It also provides Web-based analytical tools that allow researchers to carry out phasing and imputation consistently and efficiently. PHARP is freely accessible at http://alphaindex.zju.edu.cn/PHARP/index.php. We demonstrate its applicability for pig commercial 50K SNP arrays, by accurately imputing 2.6 billion genotypes at a concordance rate value of 0.971 in 81 Large White pigs (~ 17x sequencing coverage). We also applied our reference panel to impute the low-density SNP chip into the high-density data for three GWASs and found novel significantly associated SNPs that might be casual variants.

genomics↗

bioRxiv2021

Development and Application of Cas13a-based Diagnostic Assay for Neisseria Gonorrhoeae Detection and Identification of Azithromycin Resistance

Gonorrhea caused by Neisseria gonorrhoeae has spread world-wide. Antimicrobial-resistant strains have emerged to an alarming level to most antibiotics including to the ceftriaxone-azithromycin combination, currently recommended as first-line dual therapy. Rapid testing for antimicrobial resistance will contribute to clinical decision-making for rational drug use and will slow this trend. Herein, we developed a Cas13a-based assay for N. gonorrhoeae detection (porA target) and azithromycin resistance identification (A2059G and C2611T point mutations). We evaluated the sensitivity and specificity of this method, and 10 copies per reaction can be achieved in porA detection and C2611T identification, with no cross-reactions. Comparison of the Cas13a-based assay (porA target) with Roche Cobas 4800 assay (n=23 urine samples) revealed 100% concordance. Isolated N. gonorrhoeae strains were used to validate the identification of A2059G and C2611T resistance mutations. All tested strains (8 A2059G strains, 8 C2611T strains, and 8 wild-type strains) were successfully distinguished by our assay and verified by testing MIC for azithromycin and sequencing the 23S rRNA gene. We adopted lateral flow for the SHERLOCK assay readout, which showed a visible difference between test group and NC group results. To further evaluate the capability of our assay, we tested 27 urethral swabs from patients with urethritis for N. gonorrhoeae detection and azithromycin-resistance identification. Of these, 62.96% (17/27) strains were detected with no mutant strains and confirmed by sequencing. In conclusion, the novel Cas13a-based assay for rapid and accurate N. gonorrhoeae detection combined with azithromycin drug resistance testing is a promising assay for application in clinical practice.

microbiology↗

bioRxiv2021

Phase separation of RNA-binding protein promotes polymerase engagement and transcription

An RNA-involved phase-separation model has been proposed for transcription control. Yet, the molecular links that connect RNA binding to the transcription machinery remain missing. Here we find RNA-binding proteins (RBPs) constitute half of the chromatin proteome in embryonic stem cells (ESCs), and some are colocalized with RNA polymerase (Pol) II at promoters and enhancers. Biochemical analyses of representative RBPs--such as PSPC1 and PTBP1--show that the paraspeckle protein PSPC1 not only prevents the RNA-induced premature release of Pol II, and also makes use of RNA as multivalent molecules to promote Pol II engagement and activity, by enhancing the phase separation and subsequent phosphorylation and release of polymerase condensates. In ESCs, auxin-induced acute degradation of PSPC1 leads to genome-wide defects in Pol II phosphorylation and chromatin-binding and nascent transcription. We propose that the synergistic interplay of RBPs and RNA aids in the rate-limiting step of polymerase condensate formation to promote active transcription.

biochemistry↗

bioRxiv2021

A pipelining mechanism supporting previewing during visual exploration and reading

Humans have a remarkable ability to efficiently explore visual scenes and text by means of eye-movements. Humans typically make eye-movements (saccades) every ~250ms. Since the saccadic motor planning and execution takes 100ms this leaves only ~150ms to recognize the fixated object (or word), while simultaneously previewing candidates for the next saccade goal. We propose a pipelining mechanism that efficiently can coordinate visual exploration and reading. The mechanism is timed by alpha oscillations that coordinate the saccades, visual recognition and previewing in the cortical hierarchy. Consequently, the neuronal mechanism supporting visual processing and saccades must be studied in unison to uncover the brain mechanism supporting visual exploration and reading. HighlightsO_LIHumans have a remarkable ability to efficiently acquire information from visual scenes and pages of text by means of saccadic exploration. C_LIO_LIVisual exploration is surprisingly efficient given the temporal and spatial constraints imposed by the visual system. As such, both information from current fixations as well as upcoming locations must be processed within a 150 ms time window. C_LIO_LINew data recording in humans and non-human primates points to a link between the timing of saccades and alpha oscillations. C_LIO_LIWe present a framework in which visual exploration and reading are supported by similar neuronal mechanisms. C_LIO_LIWe propose a novel mechanism in which visual exploration and reading is supported by a pipelining mechanism organized by alpha oscillations. C_LIO_LIAccording to the pipelining mechanism, fixated and previewed objects/words are represented at different phases of an alpha cycle. C_LI

neuroscience↗

bioRxiv2021

Destruction of DNA-binding proteins by programmable O'PROTAC: Oligonucleotide-based PROTAC

DNA-binding proteins including transcription factors (TFs) play essential roles in gene transcription and DNA replication and repair during normal organ development and pathogenesis of diseases such as cancer, cardiovascular disease and obesity, deeming to be a large repertoire of attractive therapeutic targets. However, this group of proteins are generally considered undruggable as they lack an enzymatic catalytic site or a ligand binding pocket. PROteolysis-TArgeting Chimera (PROTAC) technology has been developed by engineering a bifunctional small molecule chimera to bring a protein of interest (POI) to the proximity of an E3 ubiquitin ligase, thus inducing the ubiquitination of POI and further degradation through proteasome pathway. Here we report the development of Oligonucleotide-based PROTAC (OPROTACs), a class of noncanonical PROTACs in which a TF-recognizing double-stranded oligonucleotide is incorporated as a binding moiety of POI. We demonstrate that OPROTACs of ERG and LEF1, two highly cancer-related transcription factors selectively promote degradation of these proteins and inhibit their transcriptional activity in cancer cells. The programmable nature of OPROTACs indicates that this approach is applicable to destruct other TFs. OPROTACs not only can serve as a research tool, but also can be harnessed as a therapeutic arsenal to target DNA binding proteins for effective treatment of diseases such as cancer.

biochemistry↗

bioRxiv2021

Sleep deprivation exacerbates seizures and diminishes GABAergic tonic inhibition

Patients with epilepsy report that sleep deprivation is a common trigger for breakthrough seizures. The basic mechanism of this phenomenon is unknown. In the Kv1.1-/- mouse model of epilepsy, daily sleep deprivation indeed exacerbated seizures though these effects were lost after the 3rd day. Sleep deprivation also accelerated mortality in ~52% of Kv1.1-/- mice, not observed in controls. Voltage-clamp experiments on the day after recovery from sleep deprivation showed reductions in GABAergic tonic inhibition in dentate granule cells both in Kv1.1-/- and wild-type mice. Our results suggest that sleep deprivation is detrimental to seizures and survival, possibly due to reductions in GABAergic tonic inhibition.

neuroscience↗

bioRxiv2021

Instructor-learner neural synchronization during elaborated feedback predicts learning transfer

The provision of feedback with complex information beyond the correct answer, i.e., elaborated feedback, can powerfully shape learning outcomes such as transfer, i.e., the ability to extend what has been learned in one context to new contexts. However, an understanding of neurocognitive processes of elaborated feedback during instructor-learner interactions remains elusive. Here, a two-person interactive design is used during simultaneous recording of functional near-infrared spectroscopy (fNIRS) signals from adult instructor-learner dyads. Instructors either provided elaborated feedback (i.e., correct answer and an example) or simple feedback (i.e., correct answer only) to learners during a concept learning task. Our results showed that elaborated feedback produced comparable levels of retention to simple feedback, however, transfer was significantly enhanced by elaboration. We also noted significant instructor-learner neural synchronization in frontoparietal regions during the provision of elaborated feedback, especially when examples were provided. Further, interpersonal neural synchronization in the parietal cortex successfully predicted transfer of knowledge to novel contexts. This prediction was retained for both learner-delayed and learner-preceding neural synchronization. These findings point toward transfer effects of elaborated feedback provided in a social context can be predictable through interpersonal neural synchronization, which may hold important implications for real-world learning and pedagogical efficacy. Educational Impact and Implications StatementFeedback provides learners with crucial information regarding the gap between what has currently been achieved and what remains to be achieved, and thus plays a critical role in any learning process. In real-world settings, feedback is typically provided and received through social interaction, and high-quality "elaborated feedback" contains complex information that goes beyond the correct answer. This study aims to elucidate the neurocognitive processes underpinning elaborated feedback during instructor-learner interactions. We detected significant instructor-learner neural synchronization in mutual frontoparietal brain regions during elaborated feedback, particularly during the provision of specific elaborated information (i.e., concrete examples). Moreover, this synchronization (including learner-delayed and learner-preceded synchronization) in the parietal region predicted whether the learners transferred learning to novel examples of learned psychology concepts. This study advances current understanding on the neural mechanisms for elaborated feedback and the role of social interaction in feedback effects. These results may have important implications for successful real-world learning and communication, and related pedagogical applications in educational settings.

scientific communication and education↗

bioRxiv2020

Cholecystokinin-like Peptide Mediates Satiety by Inhibiting Sugar Attraction

Feeding is essential for animal survival and reproduction and is regulated by both internal states and external stimuli. However, little is known about how internal states influence the perception of external sensory cues that regulate feeding behavior. Here, we investigated the neuronal and molecular mechanisms behind nutritional state-mediated regulation of gustatory perception in control of feeding behavior in the brown planthopper and Drosophila. We found that feeding increases the expression of the cholecystokinin-like peptide, sulfakinin (SK), and the activity of a set of SK-expressing neurons. Starvation elevates the transcription of the sugar receptor Gr64f and SK negatively regulates the expression of Gr64f in both insects. This Gr64f regulation is by direct action of SK neurons on Gr64f-expressing neurons of the proboscis and proleg tarsi that co-express the SK receptor CCKLR-17D3. Our findings thus demonstrate how nutritional state induces peptide signaling to modulate sweet perception and thereby feeding behavior.

neuroscience↗

bioRxiv2020

Lexical parafoveal previewing predicts reading speed

While reading is an essential human skill, many of the neuronal mechanisms supporting reading are not well understood. In spite of the reduced visual acuity, parafoveal information plays a critical role in natural reading1; however, it is strongly debated whether words are previewed parafoveally at the lexical level2-9. This is a key dispute for competing models on reading and of great significance since lexical retrieval is important for guiding eye movements. We found evidence for parafoveal previewing at the lexical level by combining a novel rapid invisible frequency tagging (RIFT)10, 11 approach with magnetoencephalography (MEG) and eye-tracking. In a silent reading task, target words of either low or high lexical frequency were tagged (flickered) subliminally at 60 Hz. The tagging response measured when fixating on the pre-target word reflected parafoveal previewing of the target word. We observed a stronger tagging response as early as 100 ms following fixations on pre-target words that were followed by target words of low compared with high lexical frequency. Moreover, the difference in tagging response with respect to target lexicality predicted individual reading speed. Our findings demonstrate that reading unfolds in the fovea and parafovea simultaneously to support fluent reading.

neuroscience↗

bioRxiv2020

Intestinal microbiota modulates adrenomedullary response through Nod1 sensing in chromaffin cells

The intestinal microbiota closely interacts with the neuroendocrine system and exerts profound effects on host physiology. Many of the molecular mechanisms underlying these interactions await discovery. Here we report that Nod1 ligand derived from intestinal bacteria directly modulates catecholamine storage and secretion in mouse adrenal chromaffin cells. The cytosolic peptidoglycan receptor Nod1 is involved in chromogranin A (CHGA) retention in dense core granules (DCGs) in chromaffin cells in a cell-autonomous manner. Mechanistically, upon recognizing its cognate ligands, Nod1 localizes to DCGs, and recruits Rab2a, which is critical for CHGA retention in DCGs. Loss of Nod1 ligands leads to a profound defect in epinephrine storage in chromaffin cells, and subsequently, less secretion upon stimulation. The intestine-adrenal medulla crosstalk bridged by Nod1 ligands modulates adrenal medullary responses during the immobilization-induced stress response in mice. Thus, our study uncovers a mechanism by which intestinal microbes directly modulate a major pathway in response to stress, which may provide further understanding of the gut-brain axis.

immunology↗

bioRxiv2020

Transcriptome analysis of potato leaves in response to infection with the necrotrophic pathogen Alternaria solani

The potato early blight was caused by Alternaria solani (Aso). At present, potato early blight resistant varieties are lacking. The experiment of Aso inoculation on a.k.a. Favorita showed that the content of chlorophyll decreased continuously within 2 days after inoculation. In addition, the contents of JA-Ile, SA, ABA and IAA were determined by LC-MS.The results of two defense-related hormones showed that jasmonic acid content decreased significantly, while jasmonic acid content did not change significantly. In order to understand the difference in gene expression of potatoes infected by Aso, the 24 hpi, 36 hpi and 48 hpi transcriptome were determined. The results showed that the gene annotation and cluster analysis of DEGs revealed a variety of defense responses to Aso infection, especially the plant hormone signal transduction pathway. The differential expression of 10 DEGs was confirmed by qPCR analysis. Finally, through weighted gene co-expression network analysis (WGCNA), "samonl" was determined as a key hormone-related network in the process of Aso infection in potatoes. This study provides an important clue for understanding the interaction between potato and Aso and for disease resistance breeding.

plant biology↗

bioRxiv2020

Wheat transcriptome profiling reveals abscisic and gibberellic acid treatments regulate early-stage phytohormone defense signaling, cell wall fortification, and metabolic switches following Fusarium graminearum-challenge

BackgroundApplication of the wheat phytohormones abscisic acid (ABA) or gibberellic acid (GA) affect Fusarium head blight (FHB) disease severity; however, the molecular underpinnings of the elicited phenotypes remain unclear. Herein, the transcriptomic responses of an FHB-susceptible wheat cultivar Fielder were characterized upon treatment with ABA, an ABA receptor antagonist (AS6), or GA in the presence or absence of Fusarium graminearum (Fg) challenge. ResultsA total of 30,876 differentially expressed genes (DEGs) where identified in Fielder (26,004) and Fg (4,872). Fg challenge alone resulted in the most substantial wheat DEGs contributing to 57.2% of the total transcriptomic variation. Using a combination of topology overlap and correlation analyses, 9,689 Fg-related wheat DEGs were defined. Further enrichment analysis of the top 1% networked wheat DEGs identified critical expression changes within defense responses, cell structural metabolism, molecular transport, and membrane/lipid metabolism. Fg-challenged conditions also included the expression of a putative Fg ABA-biosynthetic cytochrome P450 and repression of wheat FUS3 for dysregulating ABA and GA crosstalk. ABA treatment alone elicited 4536 (32%) wheat DEGs common to those of the Fg-challenge, and Fg+ABA further enhanced 888 (12.5%) of them. These ABA elicited DEGs are involved in defense through both classical and non-classical phytohormone signaling and regulating cell wall structures including polyphenolic metabolism. Conversely, Fg+GA opposed 2239 (33%) Fg-elicited wheat DEGs, including modulating primary and secondary metabolism, defense responses, and flowering genes. ABA and jointly ABAFg[Fg+ABA] treatments repressed, while Fg+GA induced an over-representation of wheat DEGs mapping to chromosome 6BL. Finally, compared to Fg+ABA, co-application of Fg+AS6 did not antagonize ABA biosynthesis or signal but rather elicited antagonistic Fg (557) and wheat (11) DEGs responses directly tied to stress responses, phytohormone transport, and FHB. ConclusionsComparative transcriptomics highlight the effects of wheat phytohormones on individual pathway and global metabolism simultaneously. Application of ABA may reduce FHB severity through misregulating defense mechanisms and cell wall fortification pathways. GA application may alter primary and secondary metabolism, creating a metabolic shift to ultimately reduce FHB severity. By comparing these findings to those previously reported for four additional plant genotypes, an additive model of the wheat-Fg interaction is proposed.

genomics↗

bioRxiv2020

A targetable epigenetic vulnerability in PI3K/AKT inhibitor resistant cancers

Acquisition of resistance to PI3K/AKT-targeted monotherapy implies the existence of common resistance mechanisms independent of cancer type. Here we demonstrate that PI3K/AKT inhibitors cause glycolytic crisis, acetyl-CoA shortage and a global decrease in histone acetylation. Also, PI3K/AKT inhibitors induce drug resistance by selectively augmenting H3K27 acetylation and binding of CBP/p300 and BRD4 proteins at a subset of growth factor and receptor (GF/R) gene loci. BRD4 occupation at these loci and drug resistant cell growth are vulnerable to both bromodomain and HDAC inhibitors. Little or none occupation of HDAC proteins at the GF/R gene loci underscores the paradox that cells respond equivalently to the two classes of inhibitors with opposite modes of action. Targeting this unique epigenetic vulnerability offers two viable strategies to overcome PI3K/AKT inhibitor resistance in different cancers.

cancer biology↗

bioRxiv2020

Epigenetic Interaction between UTX and DNMT1 Regulates Diet-Induced Myogenic Remodeling in Brown Fat

Brown adipocytes share the same developmental origin with skeletal muscle. Here we find that a brown adipocyte-to-myocyte remodeling also exists in mature brown adipocytes, and is induced by prolonged high fat diet (HFD) feeding, leading to brown fat dysfunction. This process is regulated by the interaction of epigenetic pathways involving histone and DNA methylation. In mature brown adipocytes, the histone demethylase UTX maintains persistent demethylation of the repressive mark H3K27me3 at Prdm16 promoter, leading to high Prdm16 expression. PRDM16 then recruits DNA methyltransferase DNMT1 to Myod1 promoter, causing Myod1 promoter hypermethylation and suppressing its expression. The interaction between PRDM16 and DNMT1 coordinately serves to maintain brown adipocyte identity while repressing myogenic remodeling in mature brown adipocytes, thus promoting their active brown adipocyte thermogenic function. Suppressing this interaction by HFD feeding induces brown adipocyte-to-myocyte remodeling, which limits brown adipocyte thermogenic capacity and compromises diet-induced thermogenesis, leading to the development of obesity.

physiology↗

bioRxiv2020

fruitless tunes functional flexibility of courtship circuitry during development

Drosophila male courtship is controlled by the male-specific products of the fruitless (fruM gene and its expressing neuronal circuitry. fruM is considered a master gene that controls all aspects of male courtship. By temporally and spatially manipulating fruM expression, we found that fruM is required during a critical developmental period for innate courtship towards females, and its function during adulthood is relatively trivial. By altering or eliminating fruM expression, we generated males that are innately heterosexual, homosexual, bisexual, or without innate courtship but could acquire such behavior in an experience-dependent manner. These findings show that fruM is not absolutely necessary for courtship but is critical during development to build a sex circuitry with reduced flexibility and enhanced efficiency and provide a new view about how fruM tunes functional flexibility of a sex circuitry.

neuroscience↗

bioRxiv2020

TRACE-Seq Reveals Clonal Reconstitution Dynamics of Gene Targeted Human Hematopoietic Stem Cells

Targeted DNA correction of disease-causing mutations in hematopoietic stem and progenitor cells (HSPCs) may usher in a new class of medicines to treat genetic diseases of the blood and immune system. With state-of-the-art methodologies, it is now possible to correct disease-causing mutations at high frequencies in HSPCs by combining ribonucleoprotein (RNP) delivery of Cas9 and chemically modified sgRNAs with homologous DNA donors via recombinant adeno-associated viral vector serotype six (AAV6). However, because of the precise nucleotide-resolution nature of gene correction, these current approaches do not allow for clonal tracking of gene targeted HSPCs. Here, we describe Tracking Recombination Alleles in Clonal Engraftment using sequencing (TRACE-Seq), a novel methodology that utilizes barcoded AAV6 donor template libraries, carrying either in-frame silent mutations or semi-randomized nucleotide sequences outside the coding region, to track the in vivo lineage contribution of gene targeted HSPC clones. By targeting the HBB gene with an AAV6 donor template library consisting of [~]20,000 possible unique exon 1 in-frame silent mutations, we track the hematopoietic reconstitution of HBB targeted myeloid-skewed, lymphoid-skewed, and balanced multi-lineage repopulating human HSPC clones in immunodeficient mice. We anticipate that this methodology has the potential to be used for HSPC clonal tracking of Cas9 RNP and AAV6-mediated gene targeting outcomes in translational and basic research settings.

molecular biology↗

bioRxiv2020

High-Speed AFM directly visualizes conformational dynamics of the HIV-Vif protein complex

Viral infectivity factor (Vif) is a protein that is essential for the replication of the HIV-1 virus. The key function of Vif is to disrupt the antiviral activity of APOBEC3 proteins, which mutate viral nucleic acids. Inside the cell, Vif binds to the host cell proteins Elongin-C, Elongin-B, and CBF-{beta}, forming a four-protein complex called VCBC. The structure of VCBC in complex with the Cullin5 (Cul5) protein has been solved by X-ray crystallography, and recently, using molecular dynamic (MD) simulations, the dynamics of VCBC and VCBC-Cul5 complexes were characterized. Here, we applied time-lapse high-speed atomic force microscopy (HS-AFM) to visualize the conformational changes of the VCBC complex. We determined the three most favorable conformations of the VCBC complex, which we identified as triangle, dumbbell, and globular structures. In addition, we characterized the dynamics of each of these structures. While our data show a very dynamic behavior for all these structures, we found the triangle and dumbbell structures to be the most dynamic. These findings provide insight into the structure and dynamics of the VCBC complex and support further research into the improvement of HIV treatment, as Vif is essential for virus survival in the cell.

biophysics↗

bioRxiv2020

Cytotoxic effects of tRNA-derived fragments and tRNA halves from non-pathogenic Escherichia coli strain on colorectal cancer cells

Transfer RNAs (tRNAs) purified from non-pathogenic E. coli strain (NPECS) possess cytotoxic properties on colorectal cancer cells. In the present study, the bioactivity of tRNA halves and tRNA fragments (tRFs) derived from NPECS are investigated for their anticancer potential. Both tRNA halves and tRF mimics studied exhibited significant cytotoxicity on colorectal cancer cells, with the latter being more effective suggesting that tRFs may be important contributors to the bioactivities of tRNAs derived from gut microbiota. Through high-throughput screening, EC83 mimic, a double-strand RNA with a 22 nt 5-tRF derived from tRNA-Leu(CAA) as antisense chain, was identified as one with the highest potency (IC50=52 nM). Structure-activity investigations revealed that 2-O-methylation of the ribose of guanosine may enhance the cytotoxic effects of EC83 mimic via increasing the stability of its tertiary structure. Consistently, 4-thiouridine substitution reversed this increased stability and the enhanced cytotoxic effects. This provides the first evidence that the bioactivity of tRF mimics would be impacted by chemical modifications. Furthermore, the present study provides the first evidence to suggest that novel tRNA fragments derived from the gut microbiota may possess anti-cancer properties and have the potential to be potent and selective therapeutic molecules. IMPORTANCEWhile the gut microbiota has been increasingly recognized to be of vital importance to human health and disease, the current literature shows that there is a lack of attention given on the non-pathogenic Escherichia coli strain. Moreover, the biological activities of tRNA fragments (tRFs) derived from bacteria have rarely been investigated. The findings from this study revealed tRFs as a new class of bioactive constituents derived from gut microorganisms, suggesting that studies on biological functional molecules in intestinal microbiota should not neglect tRFs. The research of tRFs would play an important role in biological research of gut microorganisms, including bacteria-bacteria interaction, gut-brain axis, gut-liver axis, etc. Furthermore, the guidance on the rational design of tRF therapeutics provided in this study indicates that further investigations should pay more attention to these therapeutics from probiotics. The innovative drug research of tRFs as potent druggable RNA molecules derived from intestinal microorganisms would open a new area in biomedical sciences.

microbiology↗