Biology subjects

Gu, L.

Publications and source records attributed to Gu, L..

At least 73 records · Page 4Linked to original sources

bioRxiv2022

Integrated analysis of single-cell transcriptome of liver cancer and cirrhosis reveals cell lineage similarity and prognostic-associated subpopulations

Background & AimsLiver cancer is one of the most leading causes of cancer deaths. Cirrhosis is an important risk factor for liver cancer, which is the result of over-fibrosis caused by diffuse and long-term liver damage. Despite extensive research, a systematic study for characterizing similarity between liver cancer and cirrhosis at single cell resolution is still lacking. MethodsWe established a data analysis framework to elucidate cell lineage similarity between liver cancer and cirrhosis to discover prognostic-associated subpopulations. We integrated single-cell transcriptome data from liver samples at normal, cirrhotic and cancer conditions, which totally contained 78,000 cells. Gene regulation analysis, cellular interactions and trajectory analysis were performed to characterize cirrhosis-like cell subpopulations. Bulk transcriptomes were used to discover prognostic-associated subpopulations. ResultsBy aligning cellular subpopulations across different samples, we found remarkable similarity between KNG1+ hepatocytes in cirrhosis and PGA5+ hepatocytes in HCC. Furthermore, gene regulation analysis and cellular interactions implicated E2F1, FOXA2, EGF, CDH and ANGPTL signaling in maintaining cirrhosis-like ecosystem. Strikingly, subpopulations with higher expression of cirrhosis-like signatures were associated with patients worse survival. ConclusionsWe revealed a previously unexplored cirrhosis-like ecosystem of liver cancer, which could provide novel biomarkers for therapeutic interventions in HCC. Core analysis modules in this study were integrated into a user-friendly toolkit, SIMscRNA(https://github.com/xmuhuanglab/SIM-scRNA), which could facilitate the exploration of similarity and heterogeneity between precancerous diseases and solid tumors.

bioinformatics↗

bioRxiv2022

Multi-omics of Circular RNAs and Their Responses to Hormones in Moso Bamboo (Phyllostachys edulis)

Circular RNAs are endogenous non-coding RNAs with covalently closed structures, which have important functions in plants. However, their biogenesis, degradation, and function upon treatment with gibberellins (GA) and auxins (NAA) remain unknown. Here, we systematically identified and characterized expression patterns, evolutionary conservation, genomic features, and internal structures of circRNAs using RNase R-treated libraries from moso bamboo (Phyllostachys edulis) seedlings. Moreover, we investigated the biogenesis of circRNAs dependent on both cis- and trans-regulation. We determined details regarding the function of circRNAs, including their roles in regulating microRNA-related genes and modulating the alternative splicing of their linear counterparts. Importantly, we developed a customized degradome sequencing approach to detect microRNA-mediated cleavage of circRNAs. Finally, we present a comprehensive view of the participation of circRNAs in the regulation of hormone metabolism upon treatment of bamboo seedlings with gibberellins (GA) and auxins (NAA). Collectively, our study uncovers important features of circRNAs including overall characteristics, biogenesis, function, and microRNA-mediated degradation of circRNAs in moso bamboo.

plant biology↗

bioRxiv2022

The Serotonergic Neural Circuit Between The Dorsal Raphe Nucleus And The Basolateral Amygdala Is Implicated In Modulating The Arousal from Sevoflurane Anesthesia

Although some advancements concerning the arousal involved in mediating the delayed emergency from general anesthesia, which will lead to the serious complications, had been made, the role by arousal in modulating in delayed emergency still remains to be unclear. In our models, based on our previous working that activation of the 5-Hydroxytryptamine (5-HT) neurons in the dorsal raphe nucleus (DRN) by optogenetics can significantly reduce the emergency time by activating arousal pathway, we further test whether the serotonergic neural circuit between the DRN and the basolateral amygdala (BLA) is implicated in modulating the arousal from the sevoflurane anesthesia and the emergency time of sevoflurane anesthesia by the pharmacological, optogenetics and fiber photometry. Our findings showed that whether the serotonergic neural circuit between the DRN and the basolateral amygdala (BLA) plays a key role in modulating the arousal from the sevoflurane anesthesia and the emergency time of sevoflurane anesthesia. Based on the serotonergic neural circuit, the 5-HT 1 A receptor is of great significance to mediate the arousal and the emergency time of the sevoflurane anesthesia. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/511924v2_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@34621eorg.highwire.dtl.DTLVardef@115ae09org.highwire.dtl.DTLVardef@54eb12org.highwire.dtl.DTLVardef@11515ff_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure1C_FLOATNO C_FIG

neuroscience↗

bioRxiv2022

The cytidine deaminase APOBEC3G drives cancer mutagenesis and clonal evolution in bladder cancer

Mutagenic processes leave distinct signatures in cancer genomes. The mutational signatures attributed to APOBEC3 cytidine deaminases are pervasive in human cancers. However, data linking individual APOBEC3 proteins to cancer mutagenesis in vivo are limited. Here, we show that transgenic expression of human APOBEC3G promotes mutagenesis, genomic instability, and kataegis, leading to shorter survival in a murine bladder cancer model. Acting as mutagenic fuel, APOBEC3G increases the clonal diversity of bladder cancers, driving divergent cancer evolution. We characterize the single base substitution signature induced by APOBEC3G in vivo, showing the induction of a mutational signature different from that caused by APOBEC3A and APOBEC3B. Analysis of thousands of human cancers reveals the contribution of APOBEC3G to the mutational profiles of multiple cancer types, including bladder cancer. Our findings define the role of APOBEC3G in cancer mutagenesis and clonal heterogeneity. These results potentially inform future therapeutic efforts that restrict tumor evolution.

genomics↗

bioRxiv2022

Increasing the sensitivity, recovery, and integrality of spatially resolved proteomics by LCM-MTA

Conventional proteomic approaches neglect tissue heterogeneity and spatial localization information. Laser capture microdissection (LCM) can isolate specific cell populations or histological areas from heterogeneous tissue specimens while preserving spatial localization information. Formalin-fixed paraffin-embedded (FFPE) is currently a standardized method for long-term stable preservation of clinical tissue specimens. However, spatially resolved proteomics (SRP) studies of FFPE tissues by combined LCM and mass spectrometry (MS)-based proteomics face challenges, such as formalin-induced protein crosslinking limits protein extraction and digestion, protein loss during sample preparation, and the detectability of MS for trace tissues. Therefore, it is necessary to specifically develop SRP sample preparation methods and MS methods suitable for trace FFPE tissues. Here, we provide an SRP method suitable for trace FFPE tissues produced by LCM, termed LCM-Magnetic Trace Analysis (LCM-MTA), which can significantly increase the sensitivity, recovery, and integrality of SRP. The starting material has been reduced to about 15 cells, which resolution is comparable to existing spatially resolved transcriptome (SRT). We also apply our LCM-MTA into SRP studies on clinical colorectal cancer (CRC) tissues and accurately distinguish the functional differences of different cell types. In conclusion, LCM-MTA is a convenient, universal, and scalable method for SRP of trace FFPE tissues, which can be widely used in clinical and non-clinical research fields.

systems biology↗

bioRxiv2022

Digitally Predicting Protein Localization and Manipulating Protein Activity in Fluorescence Images Using Four-dimensional Reslicing GAN

MotivationWhile multi-channel fluorescence microscopy is a vital imaging method in biological studies, the number of channels that can be imaged simultaneously is limited by technical and hardware limitations such as emission spectra cross-talk. One feasible solution is using deep neural networks to model the localization relationship between two proteins so that the localization of a protein can be digitally predicted. Furthermore, the input and predicted localization implicitly reflects the modeled relationship. Accordingly, observing the predictions via repeatedly manipulating input localizations is an explainable and feasible way to analyze the modeled relationships between the input and the predicted proteins. ResultsWe propose a Protein Localization Prediction (PLP) method using a cGAN named Four-dimensional Reslicing Generative Adversarial Network (4DR-GAN) to digitally generate additional channels. 4DR-GAN models the joint probability distribution of imaged and target proteins by simultaneously incorporating the protein localization signals in four dimensions including space and time. Because protein localization often correlates with protein activation state, with accurate PLP, we further propose two novel tools: digital activation (DA) and digital inactivation (DI) to digitally activate and inactivate a protein and observe the response of the predicted protein localization. Compared with genetic approaches, these tools allow precise spatial and temporal control. A comprehensive experiment on four groups of proteins shows that 4DR-GAN achieves higher-quality PLP than Pix2Pix and the DA and DI responses are consistent with the known protein functions. The proposed PLP method helps simultaneously visualize additional proteins and DA and DI provide guidance to study localization-based protein functions. Availability and ImplementationThe open-source code is at https://github.com/YangJiaoUSA/4DR-GAN.

bioinformatics↗

bioRxiv2022

A diverse network of pericoerulear neurons control arousal states

As the primary source of norepinephrine (NE) in the brain, the locus coeruleus (LC) regulates arousal, avoidance and stress responses1,2. However, how local neuromodulatory inputs control LC function remains unresolved. Here we identify a population of transcriptionally, spatially and functionally diverse GABAergic neurons in the LC dendritic field that receive distant inputs and modulate modes of LC firing to control global arousal levels and arousal-related processing and behaviors. We define peri-LC anatomy using viral tracing and combine single-cell RNA sequencing with spatial transcriptomics to molecularly define both LC-NE and peri-LC cell types. We identify several neuronal cell types which underlie peri-LC functional diversity using a series of complementary neural circuit approaches in behaving mice. Our findings indicate that LC and peri-LC neurons are transcriptionally, functionally, and anatomically heterogenous neuronal populations which modulate arousal and avoidance states. Defining the molecular, cellular, and functional diversity of the LC and peri-LC provides a road map for understanding the neurobiological basis of arousal, motivation and neuropsychiatric disorders.

neuroscience↗

bioRxiv2022

BigNeuron: A resource to benchmark and predict best-performing algorithms for automated reconstruction of neuronal morphology

BigNeuron is an open community bench-testing platform combining the expertise of neuroscientists and computer scientists toward the goal of setting open standards for accurate and fast automatic neuron reconstruction. The project gathered a diverse set of image volumes across several species representative of the data obtained in most neuroscience laboratories interested in neuron reconstruction. Here we report generated gold standard manual annotations for a selected subset of the available imaging datasets and quantified reconstruction quality for 35 automatic reconstruction algorithms. Together with image quality features, the data were pooled in an interactive web application that allows users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and reconstruction data, and benchmarking of automatic reconstruction algorithms in user-defined data subsets. Our results show that image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. By benchmarking automatic reconstruction algorithms, we observed that diverse algorithms can provide complementary information toward obtaining accurate results and developed a novel algorithm to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms. Finally, to aid users in predicting the most accurate automatic reconstruction results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic reconstructions.

bioinformatics↗

bioRxiv2022

Building an atlas of transposable elements reveals the extensive roles of young SINE in gene regulation, genetic diversity, and complex traits in pigs

Transposable elements (TEs) are an extensive source of genetic polymorphisms and play an indispensable role in chromatin architecture, transcriptional regulatory networks, and genomic evolution. The pig is an important source of animal protein and serves as a biomedical model for humans, yet the functional role of TEs in pigs and their contributions to complex traits are largely unknown. Here, we built a comprehensive catalog of TEs (n = 3,087,929) in pigs by a newly developed pipeline. Through integrating multi-omics data from 21 tissues, we found that SINEs with different ages were significantly associated with genomic regions with distinct functions across tissues. The majority of young SINEs were predominantly silenced by histone modifications, DNA methylation, and decreased accessibility. However, the expression of transcripts that were derived from the remaining active young SINEs exhibited strong tissue specificity through cross-examining 3,570 RNA-seq from 79 tissues and cell types. Furthermore, we detected 211,067 polymorphic SINEs (polySINEs) in 374 individuals genome-wide and found that they clearly recapitulated known patterns of population admixture in pigs. Out of them, 340 population-specific polySINEs were associated with local adaptation. Mapping these polySINEs to genome-wide associations of 97 complex traits in pigs, we found 54 candidate genes (e.g., ANK2 and VRTN) that might be mediated by TEs. Our findings highlight the important roles of young SINEs in functional genomics and provide a supplement for genotype-to-phenotype associations and modern breeding in pigs.

genomics↗

bioRxiv2022

Enhancement of central norepinephrinergic neurotransmission contributes to inhibition of seizure-induced respiratory arrest by targeting the beta-1 adrenergic receptor (β1-AR) locating in the cardiomyocytes in the DBA/1 mouse SUDEP model

Sudden unexpected death of epilepsy (SUDEP) is the leading cause of of death in patients with epilepsy. Due to the complicated pathogenesis of SUDEP, however, the exact mechanism of SUDEP remains elusive. Currently, although it is recognized that the seizure-induced respiratory arrest (S-IRA) may be a main cause for SUDEP, other factors resulting in SUDEP can not be excluded e.g arrhythmias. Our previous findings indicated that the incidence of S-IRA and SUDEP evoked by acoustic stimulation or pentetrazol (PTZ) injection was significantly reduced by atomoxetine, a norepinephrine reuptake inhibitor (NRI), suggesting that noradrenergic neurotransmission modulates S-IRA and SUDEP. Given that norepinephrine acts on the target to modulate respiratory and circulation function by targeting adrenergic receptor and beta (a-AR and {beta}-AR) and the arrhythmias can be contributed to SUDEP. Meanwhile, to further test whether cardiac factors are implicated in S-IRA and SUDEP, we choose esmolol hydrochloride, a selective antagonist of {beta}1-AR to test it in our models. Our findings demonstrated that the lower incidence of S-IRA and SUDEP evoked by acoustic stimulation or PTZ injection in DBA/1 mice by administration with atomoxetine was significantly reversed by intraperitoneal (IP) of esmolol hydrochloride. Importantly, the data of electrocardiogram (ECG) showed that the cardiac arrhythmia including the ventricular tachycardia, ventricular premature beat and atrioventricular block can be evoked by acoustic stimulation or PTZ injection in our model. Administration of atomoxetine significantly reduced these arrhythmias and the incidence of S-IRA and SUDEP in our models. However, administration of esmolol hydrochloride with the dose without affecting ECG and mortality changing of DBA/1 significantly blocking the protective effects of atomoxetine on S-IRA and SUDEP in our models. Thus, the dysfunction of respiratory and circulation may be implicated in the pathogenesis of S-IRA and SUDEP. Enhancing the central norepinephrinergic neurotransmission in the brain contributes to inhibition of seizure-induced respiratory arrest by targeting {beta}1-AR locating in the cardiomyocytes. Furthermore, the suppression effects of S-IRA by atomoxetine was significantly reversed by the norepinephrine neuronal degradation in the LC in our models. Furthermore, PTZ-induced Tyrosine hydroxylase (TH), the rate-limiting enzyme in the synthesis of norepinephrine, activity but not TH content from the serum of left ventricle and the whole heart tissue was reduced following the S-IRA. Our findings will show a new light on decoding the pathogenesis of SUDEP concerning the pathway between the LC and heart.

neuroscience↗

bioRxiv2022

An ultra-sensitive and easy-to-use multiplexed single-cell proteomic analysis

Proteins analysis from an average cell population often overlooks the cellular heterogeneity of expressed effector molecules, and knowledge about the regulations of key biological processes may remain obscure. Therefore, the necessity of single-cell proteomics (SCP) technologies arises. Without microfluidic chip, expensive ultrasonic equipment, or reformed liquid chromatogram (LC) system, we established an Ultra-sensitive and Easy-to-use multiplexed Single-Cell Proteomic workflow (UE-SCP). Specifically, the flexible sorting system ensured outstanding cell activity, high accuracy, remarkable efficiency, and robustness during single-cell isolation. Multiplex isobaric labeling realized the high-throughput analysis in trapped ion mobility spectrometry coupled with quadrupole time-of-flight mass spectrometry (timsTOF MS). Using this pipeline, we achieved single-cell protein quantities to a depth of over 2,000 protein groups in two human cell lines, Hela and HEK-293T. A small batch experiment can identify and quantify more than 3200 protein groups in 32 single cells, while a large batch experiment can identify and quantify about 4000 protein groups in 96 single cells. All the 128 single cells from different cell lines could been unsupervised clustered based on their proteomes. After the integration of data quality control, data cleaning, and data analysis, we are confident that our UE-SCP platform will be easy-to-marketing popularization and will promote biological applications of single-cell proteomics.

systems biology↗

bioRxiv2021

Recent selection is a major force driving cancer evolution

Cancer is one of the most threatening diseases to humans. Understanding the evolution of cancer genes is helpful for therapy management. However, systematic investigation of the evolution of cancer driver genes is sparse. Using comparative genomic analysis, population genetics analysis and computational molecular evolutionary analysis, we detected the evolution of 568 cancer driver genes of 66 cancer types across the primate phylogeny (long timescale selection), and in modern human populations from the 1000 human genomics project (recent selection). We found that recent selection pressures, rather than long timescale selection, significantly affect the evolution of cancer driver genes in humans. Cancer driver genes related to morphological traits and local adaptation are under positive selection in different human populations. The African population showed the largest extent of divergence compared to other populations. It is worth noting that the corresponding cancer types of positively selected genes exhibited population-specific patterns, with the South Asian population possessing the least numbers of cancer types. This helps explain why the South Asian population usually has low cancer incidence rates. Population-specific patterns of cancer types whose driver genes are under positive selection also give clues to explain discrepancies of cancer incidence rates in different geographical populations, such as the high incidence rate of Wilms tumour in the African population and of Ewings sarcomas in the European population. Our findings are thus helpful for understanding cancer evolution and providing guidance for further precision medicine.

evolutionary biology↗

bioRxiv2021

SARS-CoV-2 RdRp is a versatile enzyme with proofreading activity and ability to incorporate NHC into RNA by using diphosphate form molnupiravir as a substrate

The coronavirus disease 2019 (COVID-19) has been ravaging throughout the world for more than two years and has severely impaired both human health and the economy. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) employs the viral RNA-dependent RNA polymerase (RdRp) complex for genome replication and transcription, making RdRp an appealing target for antiviral drug development. Here, we reveal that RdRp can recognize and utilize nucleoside diphosphates (NDPs) as a substrate to synthesize RNAs with an efficiency of about two thirds of using nucleoside triphosphates (NTPs) as a substrate. NDPs incorporation is also template-specific and has high fidelity. Moreover, RdRp can incorporate {beta}-d-N4-hydroxycytidine (NHC) into RNA while using diphosphate form molnupiravir (MDP) as a substrate. We also observed that MDP is a better substrate for RdRp than the triphosphate form molnupiravir (MTP).

molecular biology↗

bioRxiv2021

Genome-wide H3K9 Acetylation Level Increases with Age-Dependent Senescence of Flag Leaf in Rice (Oryza sativa)

Flag leaf senescence is an important biological process that drives the remobilization of nutrients to the growing organs of rice. Leaf senescence is controlled by genetic information via gene expression and epigenetic modification, but the precise mechanism is as of yet unclear. Here, we analyzed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq) and examined its association with transcriptomes by RNA-seq during flag leaf aging in rice (Oryza sativa). We found that genome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and there was a positive correlation between the density and breadth of H3K9ac and gene expression and transcript elongation. A set of 1,249 up-regulated, differentially expressed genes (DEGs) and 996 down-regulated DEGs showing a strong relationship between temporal changes in gene expression and gain/loss of H3K9ac was observed during rice flag leaf aging. We produced a landscape of H3K9 acetylation-modified gene expression targets that includes known senescence-associated genes, metabolism-related genes, as well as miRNA biosynthesis-related genes. Our findings reveal a complex regulatory network of metabolism- and senescence-related pathways mediated by H3K9ac and also elucidate patterns of H3K9ac-mediated regulation of gene expression during flag leaf aging in rice. Significance statementGenome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and positively correlation the density and breadth of H3K9ac with transcript elongation and expression. Identified numerous H3K9 acetylation-modified gene expression targets reveal a complex regulatory network and metabolism-mediated senescence network that are associated with H3K9ac during leaf aging in rice.

plant biology↗

bioRxiv2021

Salidroside protects lipopolysaccharide-induced acute lung injury by regulating miR-145/ cytosolic phospholipase A2

Salidroside is one of the main active components from the root of Rhodiola rosea. Previous reports showed that salidroside exhibits anti-inflammatory properties, but the underlying mechanisms are not fully understood. Here, we observed the effects of salidroside on lipopolysaccharide (LPS)-induced acute lung injury (ALI) both in vivo and in vitro. As revealed by survival study, salidroside reduced mortality of rats and prolonged their survival time. Meanwhile, salidroside significantly improved LPS-induced lung histopathologic changes, decreased lung wet-to-dry and lung-to-body weight ratios, inhibited lung myeloperoxidase (MPO) activity. Salidroside also suppressed the expression of cytosolic PLA2 (cPLA2), the activity of phospholipase A2 (PLA2) in LPS-treated rats and the metabolites of PLA2 in bronchoalveolar lavage fluid (BALF), which was confirmed by results of prostaglandin E2 (PGE2), leukotriene B4 (LTB4) and thromboxane B2 (TXB2) detection. And the expression of microRNA-145 in LPS-treated rats was up-regulated by salidroside. Besides, salidroside raised the level of miR-145and reduced PLA2 activity in LPS-induced A549 cells in a concentration-dependent manner, which was obviously reversed by miR-145 inhibition. In conclusion, the current study demonstrated that salidroside exhibited a protective effect on LPS-induced ALI by inhibiting of the inflammatory response, which may involve in the up-regulation of miR-145 and the suppression of cPLA2. HighlightsO_LISalidroside reduces acute lung injury by inhibiting the increment and metabolism of phospholipase A2; C_LIO_LISalidroside inhibits LPS-induced PLA2 increase dependent on miR-145; C_LIO_LIThe inhibitory effect of Salidroside on Phospholipases A2 provides a link between the identification of new targets and potential new therapeutic agents for the treatment of acute lung injury. C_LI

pharmacology and toxicology↗

bioRxiv2021

Klebsiella pneumoniae hijacks the Toll-IL-1R protein SARM1 in a type I IFN-dependent manner to antagonize host immunity.

Many bacterial pathogens antagonize host defence responses by translocating effector proteins into cells. It remains an open question how those pathogens not encoding effectors counteract anti-bacterial immunity. Here, we show that Klebsiella pneumoniae hijacks the evolutionary conserved innate immune protein SARM1 to control cell intrinsic immunity. Klebsiella exploits SARM1 to regulate negatively MyD88 and TRIF-governed inflammation, and the activation of the MAP kinases ERK and JNK. SARM1 is required for Klebsiella induction of IL10 by fine-tuning the p38-type I IFN axis. SARM1 inhibits the activation of Klebsiella-induced absent in melanoma 2 inflammasome to limit IL1{beta} production, suppressing further inflammation. Klebsiella exploits type I IFNs to induce SARM1 in a capsule and LPS O-polysaccharide-dependent manner via TLR4-TRAM-TRIF-IRF3-IFNAR1 pathway. Absence of SARM1 reduces the intracellular survival of K. pneumonaie in macrophages whereas sarm1 deficient mice control the infection. Altogether, our results illustrate a hitherto unknown anti-immunology strategy deployed by a human pathogen.

microbiology↗

bioRxiv2021

A high resolution single molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

BackgroundAccurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single molecule long read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation or incomplete cDNA synthesis. ResultsWe present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 160k transcripts - twice that of the best current Arabidopsis transcriptome and including over 1,500 novel genes. 79% of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We developed novel methods to determine splice junctions and transcription start and end sites accurately. Mis- match profiles around splice junctions provided a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identified high confidence transcription start/end sites and removed fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provided higher resolution of transcript expression profiling and identified cold- and light-induced differential transcription start and polyadenylation site usage. ConclusionsAtRTD3 is the most comprehensive Arabidopsis transcriptome currently available. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single molecule sequencing analysis from any species.

plant biology↗

bioRxiv2021

Pseudocritical and Precritical States in Brain Dynamics

Scale-free brain dynamics under external stimuli raises an apparent paradox since the critical point of the brain dynamics locates at the limit of zero external drive. Here, we demonstrate that relaxation of the membrane potential removes the critical point but facilitates scale-free dynamics in the presence of strong external stimuli. These findings feature biological neural networks as systems that have no real critical point but bear critical-like behaviors. Attainment of such pseudocritical states relies on processing neurons into a precritical state where they are made readily activatable. We discuss supportive signatures in existing experimental observations and advise new ones for these intriguing properties. These newly revealed repertoires of neural states call for reexamination of brains working states and open fresh avenues for the investigation of critical behaviors in complex dynamical systems.

neuroscience↗