Biology subjects

Jiang, C.

Publications and source records attributed to Jiang, C..

At least 127 records · Page 7Linked to original sources

bioRxiv2022

Intrathecal administration of bone marrow stromal cells and TGF-β1 alleviate chemotherapy-induced neuropathic pain in male mice

Chemotherapy-induced peripheral neuropathy (CIPN) is the de facto clinical side effect that limits the administration of anti-cancer treatments. Recently, we reported that intrathecally injected bone marrow stromal cells (BMSCs) reduced nerve trauma-induced neuropathic pain in male mice via TGF-{beta}1 signaling. In this study, we examined sex-dependent pain relief mediated by intrathecally delivered BMSCs and TGF-{beta}1 in paclitaxel (PTX)-induced CIPN. BMSCs were prepared from primary cultures of male or female mice separately. A single intrathecal injection of BMSCs, prepared from male donors, completely prevented the development of PTX-evoked mechanical allodynia in male mice. However, female mice showed no analgesic response to either male or female BMSCs. Additionally, male mice did not demonstrate an analgesic response to BMSCs from female donors. Intrathecal injection of TGF-{beta}1 neutralizing antibody reversed the analgesic action of BMSCs. Interestingly, spinal administration of TGF-{beta}1 reduced mechanical allodynia in male mice but not in female mice. Ex vivo patch-clamp recordings in spinal cord slices revealed that TGF-{beta}1 inhibited PTX-induced synaptic plasticity, i.e. increase in spontaneous excitatory synaptic currents (sEPsCs), in spinal cord neurons from male mice only. Intrathecal TGF-{beta}1 increased the paw withdrawal threshold in von Frey testing in naive mice of males but not females, and the antinociceptive effect of TGF-{beta}1 in males was blocked by orchiectomy-induced androgen deficiency. Together, these findings reveal sex dimorphism in BMSC control of mechanical pain through spinal TGF-{beta}1 signaling.

neuroscience↗

bioRxiv2022

Processing UMI Datasets at High Accuracy and Efficiency with the Sentieon ctDNA Analysis Pipeline

Liquid biopsy enables identification of low allele frequency (AF) tumor variants and novel clinical applications such as minimum residual disease (MRD) monitoring. However, challenges remain, primarily due to limited sample volume and low read count of low-AF variants. Because of the low AFs, some clinically significant variants are difficult to distinguish from errors introduced by PCR amplification and sequencing. Unique Molecular Identifiers (UMIs) have been developed to further reduce base error rates and improve the variant calling accuracy, which enables better discrimination between background errors and real somatic variants. While multiple UMI-aware ctDNA analysis pipelines have been published and adopted, their accuracy and runtime efficiency could be improved. In this study, we present the Sentieon ctDNA pipeline, a fast and accurate solution for small somatic variant calling from ctDNA sequencing data. The pipeline consists of four core modules: alignment, consensus generation, variant calling, and variant filtering. We benchmarked the ctDNA pipeline using both simulated and real datasets, and found that the Sentieon ctDNA pipeline is more accurate than alternatives.

bioinformatics↗

bioRxiv2022

A Tailored Approach To Study Legionella Infection Using Lattice Light Sheet Microscope (LLSM)

Legionella is a genus of ubiquitous environmental pathogens found in freshwater systems, moist soil, and composted materials. More than four decades of Legionella research has provided important insights into Legionella pathogenesis [1]. Although standard commercial microscopes have led to significant advances in understanding Legionella pathogenesis [2,3], great potential exists in the deployment of more advanced imaging techniques to provide additional insights. The Lattice Light Sheet Microscope (LLSM) is a recently developed microscope for 4D live cell imaging with high resolution and minimum photo-damage [4]. We built a LLSM with an improved version for the optical layout with two path-stretching mirror sets and a novel Reconfigurable Galvanometer Scanner (RGS) module to improve the reproducibility and reliability of the alignment and maintenance of the LLSM. We commissioned this LLSM to study Legionella pneumophila infection with a tailored workflow designed over instrumentation, experiments, and data processing methods. Our results indicate that Legionella pneumophila infection is correlated with a series of morphological signatures such as smoothness, migration pattern and polarity both statistically and dynamically. Our work demonstrates the benefits of using LLSM for studying long-term questions in bacterial infection. Our free-for-use modifications and workflow designs on the use of LLSM system contributes to the adoption and promotion of the state-of-the-art LLSM technology for both academic and commercial applications.

bioengineering↗

bioRxiv2022

Invasiveness of Cancer Populations in a Two-dimensional Percolation cluster: a Stochastic Mathematical Approach

A framework for the software Unstructured Reaction-Diffusion Master Equation (URDME) was developed. A mitogenic paracrine signaling pathway was introduced phenomenologically to show how cells cooperate with one another. We modeled the emerging Allee effect using low seeding density culture (LSDC) assays to fit the model parameters. Finite time scaling (FTS) was found to be a useful tool for quantifying invasiveness in cancer populations. Through simulation, we analyzed the growth-migration dynamics of BT474 cancer cell populations in-vitro in a 2D percolation cluster and calculated the SPR (successful penetration rate). By analyzing the temporal trajectories of the SPR, we could determine the critical exponents of the critical SPR scaling relation [Formula]. Moreover, the SPR transition point defined according to the FTS theory, Pc, is negatively correlated with the invasiveness of cancer cell populations. The Pc of the three virtual cancer populations distinctly designated by varying the parameter set of the same model are 0.3408, 0.3675, and 0.4454, respectively. Therefore, the FTS algorithm may be useful in determining invasiveness. Through the simplistic phenomenological paracrine model, inter-cell cooperation and mutual mitogenic boosting are enabled, causing the Allee effect to occur. Such a method could be applied to other circumstances as an example of the quantitatively falsifiable emerging theory.

cancer biology↗

bioRxiv2022

A CRISPR screen identifies redox vulnerabilities for KEAP1/NRF2 mutant non-small cell lung cancer

The redox regulator NRF2 is hyperactivated in a large percentage of non-small cell lung cancer (NSCLC) cases, which is associated with chemotherapy and radiation resistance. To identify redox vulnerabilities for KEAP1/NRF2 mutant NSCLC, we conducted a CRISPR-Cas9-based negative selection screen for antioxidant enzyme genes whose loss sensitized cells to sub-lethal concentrations of the superoxide (O2*-)-generating drug {beta}-Lapachone. While our screen identified expected hits in the pentose phosphate pathway, the thioredoxin-dependent antioxidant system, and glutathione reductase, we also identified the mitochondrial superoxide dismutase 2 (SOD2) as one of the top hits. Surprisingly, {beta}-Lapachone did not generate mitochondrial O2*- but rather SOD2 loss enhanced the efficacy of {beta}-Lapachone due to loss of iron-sulfur protein function, loss of mitochondrial ATP maintenance and deficient NADPH production. Importantly, inhibition of mitochondrial electron transport activity sensitized to {beta}-Lapachone, demonstrating these effects may be translated to increase ROS sensitivity therapeutically.

cancer biology↗

bioRxiv2021

Non-rapid eye movement sleep and wake neurophysiology in schizophrenia

Motivated by the potential of objective neurophysiological markers to index thalamocortical function in patients with severe psychiatric illnesses, we comprehensively characterized key NREM sleep parameters across multiple domains, their interdependencies, and their relationship to waking event-related potentials and symptom severity. In 130 schizophrenia (SCZ) patients and controls, we confirmed a marked reduction in sleep spindle density in SCZ and extended these findings to show that only slow spindles predicted symptom severity, and that fast and slow spindle properties were largely uncorrelated. We also describe a novel measure of slow oscillation and spindle interaction that was attenuated in SCZ. The main sleep findings were replicated in a demographically distinct sample, and a joint model, based on multiple NREM components, predicted disease status in the replication cohort. Although also altered in patients, auditory event-related potentials elicited during wake were unrelated to NREM metrics. Consistent with a growing literature implicating thalamocortical dysfunction in SCZ, our characterization identifies independent NREM and wake EEG biomarkers that may index distinct aspects of SCZ pathophysiology and point to multiple neural mechanisms underlying disease heterogeneity. This study lays the groundwork for evaluating these neurophysiological markers, individually or in combination, to guide efforts at treatment and prevention as well as identifying individuals most likely to benefit from specific interventions.

neuroscience↗

bioRxiv2021

A calibrated functional patch clamp assay to enhance clinical variant interpretation in KCNH2-related long QT syndrome

PurposeModern sequencing technologies have revolutionised our detection of gene variants. In most genes, including KCNH2, the majority of missense variants are currently classified as variants of uncertain significance (VUS). The aim of this study is to investigate the utility of an automated patch-clamp assay for aiding clinical variant classification in the KCNH2 gene. MethodsThe assay was designed according to recommendations of the ClinGen sequence variant interpretation framework. Thirty-one control variants of known clinical significance (17 pathogenic/likely pathogenic, 14 benign/likely benign) were heterozygously expressed in Flp-In HEK293 cells. Variants were analysed for effects on current density and channel gating. A panel of 44 VUS was then assessed for reclassification. ResultsAll 17 pathogenic variant controls had reduced current density and 13/14 benign variant controls had normal current density, which enabled determination of normal and abnormal ranges for applying moderate or supporting evidence strength for variant classification. Inclusion of KCNH2 functional assay evidence enabled us to reclassify 6 out of 44 VUS as likely pathogenic. ConclusionThe high-throughput patch clamp assay can provide moderate strength evidence for clinical interpretation of clinical KCNH2 variants and demonstrates the value proposition for developing automated patch clamp assays for other ion channel genes.

genetics↗

bioRxiv2021

Mitogen-activated protein kinases associated sites of tobacco REPRESSION OF SHOOT GROWTH regulates its localization in plant cells

Plant defense and growth rely on multiple transcriptional factors (TFs). REPRESSION OF SHOOT GROWTH (RSG) is known as one of the important TFs in tobacco (Nicotiana tabacum) with a basic leucine zipper domain. RSG was involved in plant gibberellin feedback regulation by inducing the expression of key genes. The tobacco calcium-dependent protein kinase, CDPK1 was reported to interact with RSG and manipulate its intracellular localization by phosphorylating Ser-114 of RSG. Here, we identified tobacco mitogen-activated protein kinase 3 (NtMPK3) as a RSG interacted protein kinase. Mutation of predicted MAPK-associated phosphorylation site of RSG (Thr-30, Ser-74 and Thr-135) significantly altered the intracellular localization of NtMPK3-RSG interaction complex. Nuclear transport of RSG and its amino acids mutants (T30A and S74A) were observed after treated with plant defense elicitor peptide flg22 in 5 min, while the two mutated RSG swiftly relocalized in tobacco cytoplasm in 30 min. Moreover, triple points mutation of RSG (T30A/S74A/T135A) mimics constant unphosphorylated status, and predominantly localized in tobacco cytoplasm. RSG (T30A/S74A/T135A) showed no relocalization effect under the treatments of either flg22, B. cereus AR156 or GA3, and was impaired in its role as TFs. Our results suggest that MAPK associated phosphorylation sites of RSG regulate its localization in tobacco and constant unphosphorylation of RSG in Thr-30, Ser-74 and Thr-135 keeps RSG predominantly localized in cytoplasm.

physiology↗

bioRxiv2021

Landscape, complexity and regulation of a filamentous fungal transcriptome

Alternative splicing (AS) and alternative polyadenylation (APA) of pre-mRNAs contribute greatly to transcriptome complexity and gene expression regulation in higher eukaryotes. Their biological impact in filamentous fungi, however, has been poorly studied. Here we combine PacBio Isoform Sequencing and strand-specific RNA-Seq of multiple tissues together with mutant characterization to reveal the landscape, complexity and regulation of AS and APA in the filamentous plant pathogenic fungus Fusarium graminearum. We updated the reference genome and generated a comprehensive annotation comprising 51,617 transcript isoforms from 17,189 genes. Majority of the transcripts represent novel isoforms, including 2,998 undiscovered protein-coding genes. In total, 42.7% of multi-exonic genes and 64.8% of genes have AS and APA isoforms, respectively, suggesting AS and APA increase previously unrecognized transcriptome complexity in fungi. Nonsense-mediated mRNA decay factor FgUPF1 may not degrade AS transcripts with premature-stop codons but regulate ribosome biogenesis. Distal polyadenylation sites have a strong signal but proximal polyadenylation isoforms are high expressed. The core 3-end processing factors FgRNA15, FgHRP1, and FgFIP1 play important roles in promoting proximal polyadenylation site usage and also intron splicing. Genome-wide increase in the abundance of transcripts with retained introns and long 3-UTRs and downregulation of the spliceosomal and 3-end processing factors are found in older tissues and quiescent conidia, indicating that intron retention and 3-UTR lengthening may be a transcriptional signature of aging and dormancy in fungi. Overall, our study generates a comprehensive full-length transcript annotation for F. graminearum and provides new insights into the complexity and regulation of transcriptome in filamentous fungi.

genomics↗

bioRxiv2021

CsMYB4a from Camellia sinensis Regulates the Auxin Signaling Pathway by Interacting with CsIAA4

Members of the R2R3-MYB4 subgroup are well-known negative regulatory transcription factors of phenylpropane and lignin pathways. In this study, we found that transgenic tobacco plants overexpressing a R2R3-MYB4 subgroup gene from Camellia sinensis (CsMYB4a) showed inhibited growth that was not regulated by phenylpropane and lignin pathways, and these plants exhibited altered sensitivity to synthetic auxin 1-naphthaleneacetic acid (-NAA) treatment. An auxin/indole-3-acetic acid 4 (AUX/IAA4) gene from Camellia sinensis (CsIAA4) participating in the regulation of the auxin signal transduction pathway was screened from the yeast two-hybrid library with CsMYB4a as the bait protein, and tobacco plants overexpressing this gene showed a series of auxin-deficiency phenotypes, such as dwarfism, small leaves, reduced lateral roots, and a shorter primary root. CsIAA4 transgenic tobacco plants were less sensitive to exogenous -NAA than control plants, which was consistent with the findings for CsMYB4a transgenic tobacco plants. The knockout of the endogenous NtIAA4 gene (a CsIAA4 homologous gene) in tobacco plants alleviated growth inhibition in CsMYB4a transgenic tobacco plants. Furthermore, protein-protein interaction experiments proved that domain II of CsIAA4 is the key motif for the interaction between CsIAA4 and CsMYB4a and that the degradation of CsIAA4 is prevented when CsMYB4a interacts with CsIAA4. In summary, our results suggest that CsMYB4a is a multifunctional transcription factor that regulates the auxin signaling pathway, phenylpropane and lignin pathways. This study provides new insights into the multiple functions of R2R3-MYB4 subgroup members as a group of well-known negative regulatory transcription factors. One-sentence summaryCsMYB4a act as multifunctional transcription factor that regulates the auxin signaling pathway, phenylpropane and lignin pathways.

physiology↗

bioRxiv2021

Alkaliphilus flagellata sp. nov., Butyricicoccus intestinisimiae sp. nov., Clostridium mobile sp. nov., Clostridium simiarum sp. nov., Dysosmobacter acutus sp. nov., Paenibacillus brevis sp. nov., Peptoniphilus ovalis sp. nov., and Tissierella simiarum sp. nov., isolated from monkey feces

Non-human primates harbor diverse microbiomes in their guts. As a part of China Microbiome Initiatives, we cultivated and characterized the gut microbiome of cynomolgus monkeys (Macaca fascicularis). In this report, we communicate the characterization and taxonomy of 8 bacterial strains that were obtained from fecal samples of captive cynomolgus monkeys. The results revealed that they represented 8 novel bacterial species. The proposed names of the 8 novel species are Alkaliphilus flagellate (type strain MSJ-5T =CGMCC 1.45007T=KCTC 15974T), Butyricicoccus intestinisimiae MSJd-7T (type strain MSJd-7T =CGMCC 1.45013T =KCTC 25112T), Clostridium mobile (type strain MSJ-11T =CGMCC 1.45009T=KCTC 25065T), Clostridium simiarum (type strain MSJ-4T =CGMCC 1.45006T =KCTC 15975T), Dysosmobacter acutus (type strain MSJ-2T =CGMCC 1.32896T=KCTC 15976T), Paenibacillus brevis MSJ-6T (type strain MSJ-6T =CGMCC 1.45008T=KCTC 15973T), Peptoniphilus ovalis (type strain MSJ-1T =CGMCC 1.31770T=KCTC 15977T), and Tissierella simiarum (type strain MSJ-40T =CGMCC 1.45012T=KCTC 25071T).

microbiology↗

bioRxiv2021

PD-1 in hippocampal neurons regulates excitability, synaptic plasticity, and cognition

Immunotherapy using monoclonal antibodies against programmed cell death protein 1 (PD-1) demonstrated improved survival in cancer patients through immune activation. Here we show that functional PD-1 is expressed in mouse and primate hippocampal neurons and PD-1 inhibition improves cognition in physiological and pathological conditions. Mice lacking the Pdcd1 gene encoding PD-1 exhibit enhanced long-term potentiation (LTP) and learning and memory. These behavioral and cellular changes can be recapitulated by selective deletion of Pdcd1 in hippocampal excitatory neurons but not in microglia. Perfusion of mouse or nonhuman primate brain slices with anti-PD-1 antibody is sufficient to increase excitability in CA1 hippocampal neurons. Conversely, re-expression of Pdcd1 in PD-1 deficient hippocampal neurons suppresses memory and LTP. Traumatic brain injury impairs learning and memory, which is improved by intraventricular administration of anti-PD-1. These findings suggest that anti-PD-1 treatment has therapeutic potential to counteract cognitive decline. HighlightsO_LIAdult mice lacking Pdcd1 in hippocampal neurons exhibit enhanced memory and LTP C_LIO_LIAnti-PD-1 antibody treatment increases CA1 neuron excitability in brain slices of mice and primates C_LIO_LIRe-expression of Pdcd1 in PD-1 deficient hippocampal neurons impairs memory and LTP C_LIO_LICognitive deficits after traumatic brain injury are improved by anti-PD-1 treatment C_LI

neuroscience↗

bioRxiv2021

High-throughput functional analysis of CFTR and other apically localized channels in iPSC derived intestinal organoids

Induced Pluripotent Stem Cells (iPSCs) can be differentiated into epithelial organoids that recapitulate the relevant context for CFTR and enable testing of therapies targeting Cystic Fibrosis (CF)-causing mutant proteins. However, to date, CF-iPSC-derived organoids have only been used to study pharmacological modulation of mutant CFTR channel activity and not the activity of other disease relevant membrane protein constituents. In the current work, we describe a high-throughput, fluorescence-based assay of CFTR channel activity in iPSC-derived intestinal organoids and describe how this method can be adapted to study other apical membrane proteins. In these proof-of-concept studies, we show how this fluorescence-based assay of apical membrane potential can be employed to study CFTR and ENaC channels and an electrogenic acid transporter in the same iPSC-derived intestinal tissue. This multiparameter phenotypic platform promises to expand CF therapy discovery to include strategies to target multiple determinants of epithelial fluid transport.

molecular biology↗

bioRxiv2021

Survival mechanism of a novel marine multistress-tolerant Meyerozyma guilliermondii GXDK6 under high NaCl stress as revealed by integrative omics analysis

A novel strain named Meyerozyma guilliermondii GXDK6 was provided in this work, which was confirmed to survive independently under high salt stress (12% NaCl) or co-stress condition of strong acid (pH 3.0) and high salts (10% NaCl) without sterilization. Its survival mechanism under high salt stress was revealed by integrated omics for the first time. Whole-genome analysis showed that 14 genes (e.g., GPD1 and FPS1) of GXDK6 relevant to salt tolerance were annotated and known to belong to various salt-resistant mechanisms (e.g., regulation of cell signal transduction and glycerol metabolism controls). Transcriptome sequencing results indicated that 1220 genes (accounting for 10.15%) of GXDK6 were differentially transcribed (p < 0.05) when GXDK6 growth was under 10% stress for 16 h, including important novel salt-tolerant-related genes (e.g., RTM1 and YHB1). Proteomics analysis demonstrated that 1005 proteins (accounting for 27.26%) of GXDK6 were differentially expressed (p < 0.05) when GXDK6 was stressed by 10% NaCl. Some of the differentially expressed proteins were defined as the novel salt-tolerant related proteins (e.g., sugar transporter STL1 and NADPH-dependent methylglyoxal reductase). Metabolomic analysis results showed that 63 types of metabolites (e.g., D-mannose, glycerol and inositol phosphate) of GXDK6 were up- or downregulated when stressed by 10% NaCl. Among them, D-mannose is one of the important metabolites that could enhance the salt-tolerance survival of GXDK6. IMPORTANCEMicrobial contamination is a huge obstacle in industrial fermentation. The emergence of multistress-tolerant microorganism is expected to realize industrial fermentation without sterilization by controlling specific conditions. However, microorganisms eligible for non-sterile fermentation are required to survive independently under the selected special conditions for the fermentation conditions to be controlled to avoid microbial contamination. Here, a novel marine Meyerozyma guilliermondii was presented, which is able to survive well under high salt stress, its survival mechanism was systematically revealed by integrated omics technology. In addition, finding that NaCl stress could also stimulate the biosynthesis of functional metabolites from GXDK6 (e.g., calcitriol and didemnin B). Among the functional metabolites, calcitriol biosynthesis via microbial method was rarely reported. Thus, its biosynthetic mechanism was further revealed. The findings in this study contributed to understanding the survival mechanism of M. guilliermondii under high salt stress, and the development of new molecular drugs from M. guilliermondii GXDK6. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/450280v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@928135org.highwire.dtl.DTLVardef@60c713org.highwire.dtl.DTLVardef@1adb19dorg.highwire.dtl.DTLVardef@67caaa_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

Mapping the host protein interactome of non-coding regions in SARS-CoV-2 genome

A deep understanding of SARS-CoV-2-host interactions is crucial to the development of effective therapeutics. The role of non-coding regions of viral RNA (ncrRNAs) has not been scrutinized. We developed a method using MS2 affinity purification coupled with liquid chromatography-mass spectrometry (MAMS) to systematically map the interactome of SARS-CoV-2 ncrRNA in different human cell lines. Integration of the results defined the core and cell-type-specific ncrRNA-host protein interactomes. The majority of ncrRNA-binding proteins were involved in RNA biogenesis, protein translation, viral infection, and stress response. The 5' UTR interactome is enriched with proteins in the snRNP family and is a target for the regulation of viral replication and transcription. The 3' UTR interactome is enriched with proteins involved in the cytoplasmic RNP granule (stress granule) and translation regulation. We show that the ORF10 is likely to be a part of 3' UTR. Intriguingly, the interactions between negative-sense ncrRNAs and host proteins, such as translation initiation factors and antiviral factors, suggest a pathological role of negative-sense ncrRNAs. Moreover, the cell-type-specific interactions between ncrRNAs and mitochondria may explain the differences of cell lines in viral susceptibility. Our study unveils a comprehensive landscape of the functional SARS-CoV-2 ncrRNA-host protein interactome, providing a new perspective on virus-host interactions and the design of future therapeutics.

genomics↗

bioRxiv2021

FMRI multi-scale cortical spontaneous activity: 7T vs. 3T

This paper describes the use of the Human Connectome Project (HCP) data for mapping the distribution of spontaneous activity in the human brain across different spatial scales, magnets and individuals. Specifically, the resting-state functional MRI signals acquired under the HCP 3 tesla (T) and 7T magnet protocols were measured by computational methods at multiple spatial scales across the cerebral cortex using: 1) an amplitude metric on a single measuring unit (ALFF), 2) a functional homogeneity metric on a set of neighboring measuring units (ReHo) and 3) a homotopic functional connectivity metric on pairs of symmetric measuring units between the two hemispheres (VMHC). Statistical assessments on these measurements revealed that all the raw metrics were enhanced by the higher magnetic field, highlighting their dependence on magnet field strength. Measurement reliability of these global measurements were moderate to high and comparable between between 3T and 7T magnets. The differences in these measurements introduced by the higher magnetic field were spatially dependent and varied according to specific cortical regions. Specifically, the spatial contrasts of ALFF were enhanced by the 7T magnet within the anterior cortex while weakened in the posterior cortex. This is opposite for ReHo and VMHC. This scale-dependent phenomena also held true for measurement reliabilities, which were enhanced by the 7T magnet for ReHo and VMHC and weakened for ALFF. These reliability differences were primarily located in high-order associate cortex, reflecting the corresponding changes of individual differences: higher between-subject variability and lower within-subject variability for ReHo and VMHC, lower between-subject variability and higher within-subject variability for ReHo and VMHC with respect to higher magnetic field strength. Our work, for the first time, demonstrates the spatial-scale dependence of spontaneous cortical activity measurements in the human brain and their test-retest reliability across different magnet strengths, and discussed about the statistical implications for experimental design using resting-state fMRI.

neuroscience↗

bioRxiv2021

5-methylcytosine modification by Plasmodium NSUN2 stabilizes mRNA and mediates the development of gametocytes

5-methylcytosine (m5C) is an important epitranscriptomic modification involved in mRNA stability and translation efficiency in various biological processes. However, it remains unclear if m5C modification contributes to the dynamic regulation of the transcriptome during the developmental cycles of Plasmodium parasites. Here, we characterize the landscape of m5C mRNA modifications at single nucleotide resolution in the asexual replication stages and gametocyte sexual stages of rodent (P. yoelii) and human (P. falciparum) malaria parasites. While different representations of m5C-modified mRNAs are associated with the different stages, the abundance of the m5C marker is strikingly enhanced in the transcriptomes of gametocytes. Our results show that m5C modifications confer stability to the Plasmodium transcripts and that a Plasmodium ortholog of NSUN2 is a major mRNA m5C methyltransferase in malaria parasites. Upon knock-out of P. yoelii nsun2 (pynsun2), marked reductions of m5C modification were observed in a panel of gametocytogenesis-associated transcripts. These reductions correlated with impaired gametocyte production in rodent and human malaria parasites. Restoration of the nsun2 gene in the knock-out parasites rescued the gametocyte production phenotype as well as m5C modification of the gametocytogenesis-associated transcripts. Together with the mRNA m5C profiles for two species of Plasmodium, our findings demonstrate a major role for NSUN2-mediated m5C modifications in mRNA transcript stability and sexual differentiation in malaria parasites. SignificanceModifications of RNA including methylations of cytosine (m5C) and adenosine (m6A) have important roles in RNA metabolism, cellular responses to stress, and biological processes of differentiation and development. Here, we report on the profiles of m5C mRNA modifications in malaria parasites that infect rodents (Plasmodium yoelii) and humans (Plasmodium falciparum). These parasites have genes that encode homologs of human and plant NSUN2 methyltransferases (m5C "writers"). We show that one of these homologs, termed PyNSUN2, stabilizes mRNA transcripts in P. yoelii and mediates m5C-associated development of the parasite sexual stages (gametocytes). Further research on m5C and other epitranscriptomic modifications may yield new insights into molecular pathways of gametocyte development and mosquito infectivity that can be exploited to interrupt malaria transmission.

microbiology↗

bioRxiv2021

gcaPDA: A Haplotype-resolved Diploid Assembler

Generating chromosome-scale haplotype resolved assembly is important for functional studies. However, current de novo assemblers are either haploid assemblers that discard allelic information, or diploid assemblers that can only tackle genomes of low complexity. Here, we report a diploid assembler, gcaPDA (gamete cells assisted Phased Diploid Assembler), which exploits haploid gamete cells to assist in resolving haplotypes. We generate chromosome-scale phased diploid assemblies for the highly heterozygous and repetitive genome of a maize F1 hybrid using gcaPDA and evaluate the assembly result thoroughly. With applicability of coping with complex genomes and fewer restrictions on application than other diploid assemblers, gcaPDA is likely to find broad applications in studies of eukaryotic genomes.

genomics↗