Biology subjects

Ding, J.

Publications and source records attributed to Ding, J..

196 records · Page 11Linked to original sources

bioRxiv2019

Phenological matching drives wheat pest range shift under climate change

Shifting geographical ranges of crop pests and pathogens in response to climate change pose a threat to food security (1, 2). The orange wheat blossom midge (Sitodiplosis mosellana Gehin) is responsible for significant yield losses in China (3), the worlds largest wheat producer. Here we report that rising temperatures in the North China Plain have resulted in a mean northward range shift of 3.3{degrees} (58.8 km per decade) from the 1950s to 2010s, which accelerated to 91.3 km per decade after 1985 when the highly toxic pesticide hexachlorocyclohexane (HCH) was banned (4). Phenological matching between wheat midge adult emergence and wheat heading in this new expanded range has resulted in greater damage to wheat production. Around $286.5 million worth of insecticides were applied to around 19 million hectares in an attempt to minimize wheat midge damage to crops between 1985 and 2016. Despite use of these pesticides, wheat midge caused losses of greater than 0.95 million metric tons of grain during this period. Our results demonstrate the potential for indirect negative impacts of climate change on crop production and food security, and constitute the first large scale example of plant pest range shift due to global warming.

ecology↗

bioRxiv2019

HiVA: an integrative wet- and dry-lab platform for haplotype and copy number analysis of single-cell genomes

Haplotyping is imperative for comprehensive analysis of genomes, imputation of genetic variants and interpretation of error-prone single-cell genomic data. Here we present a novel sequencing-based approach for whole-genome SNP typing of single cells, and determine genome-wide haplotypes, the copy number of those haplotypes as well as the parental and segregational origin of chromosomal aberrations from sequencing- and array-based SNP landscapes of single cells. The analytical workflow is made available as an interactive web application HiVA (https://hiva.esat.kuleuven.be).

genomics↗

bioRxiv2019

HBEGF+ macrophages identified in rheumatoid arthritis promote joint tissue invasiveness and are reshaped differentially by medications

Macrophages tailor their function to the signals found in tissue microenvironments, taking on a wide spectrum of phenotypes. In human tissues, a detailed understanding of macrophage phenotypes is limited. Using single-cell RNA-sequencing, we define distinct macrophage subsets in the joints of patients with the autoimmune disease rheumatoid arthritis (RA), which affects ~1% of the population. The subset we refer to as HBEGF+ inflammatory macrophages is enriched in RA tissues and shaped by resident fibroblasts and the cytokine TNF. These macrophages promote fibroblast invasiveness in an EGF receptor dependent manner, indicating that inflammatory intercellular crosstalk reshapes both cell types and contributes to fibroblast-mediated joint destruction. In an ex vivo tissue assay, the HBEGF+ inflammatory macrophage is targeted by several anti-inflammatory RA medications, however, COX inhibition redirects it towards a different inflammatory phenotype that is also expected to perpetuate pathology. These data highlight advances in understanding the pathophysiology and drug mechanisms in chronic inflammatory disorders can be achieved by focusing on macrophage phenotypes in the context of complex interactions in human tissues. One Sentence SummaryA newly identified human macrophage phenotype from patients with the autoimmune condition RA is found to promote joint tissue invasiveness and demonstrates variable sensitivities to anti-inflammatory medications used to treat the disease.

immunology↗

bioRxiv2019

Shigella flexneri adherence factor expression in in vivo-like conditions

The Shigella species are Gram-negative, facultative intracellular pathogens that invade the colonic epithelium and cause significant diarrheal disease. Despite extensive research on the pathogen, comprehensive understanding of how Shigella initiates contact with epithelial cells remains unknown. Shigella maintains many of the same Escherichia coli adherence gene operons; however, at least one critical gene component in each operon is currently annotated as a pseudogene in reference genomes. These annotations, coupled with a lack of structures upon microscopic analysis following growth in laboratory media, have led the field to hypothesize that Shigella is unable to produce fimbriae or other \"traditional\" adherence factors. Nevertheless, our previous analyses have demonstrated that a combination of bile salts and glucose induce both biofilm formation and adherence to colonic epithelial cells. Through a two-part investigation, we first utilized various transcriptomic analyses to demonstrate that S. flexneri strain 2457T adherence gene operons are transcribed. Subsequently, we performed mutation, electron microscopy, biofilm, infection, and proteomic analyses to characterize three of the structural genes. In combination, these studies demonstrate that despite the gene annotations, S. flexneri 2457T uses adherence factors to initiate biofilm formation as well as epithelial cell contact. Furthermore, host factors, namely glucose and bile salts in the small intestine, offer key environmental stimuli required for proper adherence factor expression in S. flexneri. This research may have a significant impact on vaccine development for Shigella and further highlights the importance of utilizing in vivo-like conditions to study bacterial pathogenesis.\n\nImportanceBacterial pathogens have evolved to regulate virulence gene expression at critical points in the colonization and infection processes to successfully cause disease. The Shigella species infect the epithelial cells lining the colon to result in millions of cases of diarrhea and a significant global health burden. As antibiotic resistance rates increase, understanding the mechanisms of infection are vital to ensure successful vaccine development. Despite significant gains in our understanding of Shigella infection, it remains unknown how the bacteria initiate contact with the colonic epithelium. Most pathogens harbor multiple adherence factors to facilitate this process, but Shigella was thought to have lost the ability to produce these factors. Interestingly, we have identified conditions that mimic some features of gastrointestinal transit and enable Shigella to express adherence factors. This work highlights aspects of genetic regulation for Shigella adherence factors and may have a significant impact on future vaccine development.

microbiology↗

bioRxiv2018

Physiological and transcriptome analysis of indica rice ‘MH86’ overexpressing OsSPL14

OsSPL14, identified as IDEAL PLANT ARCHITECTURE1 (IPA1) or WEALTHY FARMERS PANICLE (WFP) gene, plays a critical role in regulating rice plant architecture. Here, the study showed that OsSPL14-overexpression transgenic rice plants had shorter growth period, short-narrow flag leaves, and thick-green leaves. Compared with wild type plant MH86, transgenic plants had higher chlorophyll a (Ca), chlorophyll b (Cb) and carotenoid (Cx) content at both seedling and maturity stage. Meanwhile, transcriptome analysis identified 473 up-regulated and 103 down-regulated genes in transgenic plant. The expression of differentially expressed genes (DEGs) involved in carotenoid biosynthesis, abscisic acid (ABA) metabolism and lignin biosynthesis increased significantly. Most of DEGs participated in \"plant hormone signal transduction\" and \"starch and sucrose metabolism\" are also up-regulated in transgenic plant. In addition, there were higher levels of ABA and gibberellin acid (GA3) in OsSPL14-overexpression transgenic plants. Moreover, the content of culm lignin, cellulose, silicon and potassium all increased dramatically. Thus, these results demonstrate that overexpression of OsSPL14 has influence on leaf development, hormone level and culm composition in rice, which provide more insight into understanding the function of OsSPL14.\n\nHighlightOsSPL14-overexpression transgenic plants showed shorter growth period, short-narrow flag leaves, and thick-green leaves. Transcript profile, abscisic acid (ABA) and gibberellin acid (GA3) level, and culm composition also changed obviously.

physiology↗

bioRxiv2018

Fast two-photon volumetric imaging of an improved voltage indicator reveals electrical activity in deeply located neurons in the awake brain

Imaging of transmembrane voltage deep in brain tissue with cellular resolution has the potential to reveal information processing by neuronal circuits in living animals with minimal perturbation. Multi-photon voltage imaging in vivo, however, is currently limited by speed and sensitivity of both indicators and imaging methods. Here, we report the engineering of an improved genetically encoded voltage indicator, ASAP3, which exhibits up to 51% fluorescence responses in the physiological voltage range, sub-millisecond activation kinetics, and full responsivity under two-photon illumination. We also introduce an ultrafast local volume excitation (ULOVE) two-photon scanning method to sample ASAP3 signals in awake mice at kilohertz rates with increased stability and sensitivity. ASAP3 and ULOVE allowed continuous single-trial tracking of spikes and subthreshold events for minutes in deep locations, with subcellular resolution, and with repeated sampling over multiple days. By imaging voltage in visual cortex neurons, we found evidence for cell type-dependent subthreshold modulation by locomotion. Thus, ASAP3 and ULOVE enable continuous high-speed high-resolution imaging of electrical activity in deeply located genetically defined neurons during awake behavior.

neuroscience↗

bioRxiv2018

Metatranscriptome profiling of the dynamic transcription of mRNA and sRNA of a probiotic Lactobacillus strain in human gut

Metatranscriptomic sequencing has recently been applied to study how pathogens and probiotics affect human gastrointestinal (GI) tract microbiota, which provides new insights into their mechanisms of action. In this study, metatranscriptomic sequencing was applied to deduce the in vivo expression patterns of an ingested Lactobacillus casei strain, which was compared with its in vitro growth transcriptomes. Extraction of the strain-specific reads revealed that transcripts from the ingested L. casei were increased, while those from the resident L. paracasei strains remained unchanged. Mapping of all metatranscriptomic reads and transcriptomic reads to L. casei genome showed that gene expression in vitro and in vivo differed dramatically. About 39% (1163) mRNAs and 45% (93) sRNAs of L. casei well-expressed were repressed after ingested into human gut. Expression of ABC transporter genes and amino acid metabolism genes was induced at day-14 of ingestion; and genes for sugar and SCFA metabolisms were activated at day-28 of ingestion. Moreover, expression of sRNAs specific to the in vitro log phase was more likely to be activated in human gut. Expression of rli28c sRNA with peaked expression during the in vitro stationary phase was also activated in human gut; this sRNA repressed L. casei growth and lactic acid production in vitro. These findings implicate that the ingested L. casei might have to successfully change its transcription patterns to survive in human gut, and the time-dependent activation patterns indicate a highly dynamic cross-talk between the probiotic and human gut including its microbe community.\n\nImportanceProbiotic bacteria are important in food industry and as model microorganisms in understanding bacterial gene regulation. Although probiotic functions and mechanisms in human gastrointestinal tract are linked to the unique probiotic gene expression, it remains elusive how transcription of probiotic bacteria is dynamically regulated after being ingested. Previous study of probiotic gene expression in human fecal samples has been restricted due to its low abundance and the presence of of closely related species. In this study, we took the advantage of the good depth of metatranscriptomic sequencing reads and developed a strain-specific read analysis method to discriminate the transcription of the probiotic Lactobacillus casei and those of its resident relatives. This approach and additional bioinformatics analysis allowed the first study of the dynamic transcriptome profiles of probiotic L casei in vivo. The novel findings indicate a highly regulated repression and dynamic activation of probiotic genome in human GI tract.

microbiology↗

bioRxiv2018

Cell lineage inference from SNP and scRNA-Seq data

Several recent studies focus on the inference of developmental and response trajectories from single cell NA-Seq (scRNA-Seq) data. A number of computational methods, often referred to as pseudo-time ordering, have been developed for this task. Recently, CRISPR has also been used to reconstruct lineage trees by inserting random mutations. However, both approaches suffer from drawbacks that limit their use. Here we develop a method to detect significant, cell type specific, sequence mutations from scRNA-Seq data. We show that only a few mutations are enough for reconstructing good branching models. Integrating these mutations with expression data further improves the accuracy of the reconstructed models. As we show, the majority of mutations we identify are likely RNA editing events indicating that such information can be used to distinguish cell types.

genomics↗

bioRxiv2018

Structural basis and mechanism of the unfolding-induced activation of an acid response chaperone HdeA

The role of protein structural disorder in biological functions is gaining increasing interests in the past decade. The bacterial acid-resistant chaperone HdeA belongs to a group of \"conditionally disordered\" protein that is activated via an order-to-disorder transition. However, the mechanism for unfolding-induced activation remains unclear due to the lack of experimental information on the unfolded state conformation and the chaperone-client interactions. Here we use advanced solution NMR methods to characterize the activated state conformation of HdeA under acidic condition and identify the client binding sites. The activated HdeA becomes largely disordered and exposes two essential hydrophobic patches of residues for client interactions. The pH-dependent chemical exchange saturation transfer (CEST) result identifies three acid-sensitive regions that act as structural locks during the activation process, revealing a multi-step activation mechanism of HdeA chaperone function at atomic level. The results highlight the role of protein disorder in chaperone function and the self-inhibitory role of ordered structures under non-stress conditions, offering new insights for further understanding the protein structure-function paradigm.

biochemistry↗

bioRxiv2018

A potential role for epigenetic processes in the acclimation response to elevated pCO2 in the model diatom Phaeodactylum tricornutum

Understanding of the molecular responses underpinning diatom responses to ocean acidification is fundamental for predicting how important primary producers will be shaped by the continuous rise in atmospheric CO2. In this study, we have analyzed global transcriptomic changes of the model diatom Phaeodactylum tricornutum following growth for 15 generations in elevated pCO2 by strand-specific RNA sequencing (ssRNA-seq). Our results indicate that no significant effects of elevated pCO2 and associated carbonate chemistry changes on the physiological performance of the cells were observed after 15 generations whereas the expression of genes encoding histones and other genes involved in chromatin structure were significantly down-regulated, while the expression of transposable elements (TEs) and genes encoding histone acetylation enzymes were significantly up-regulated. Furthermore, we identified a series of long non-protein coding RNAs (lncRNAs) specifically responsive to elevated pCO2, suggesting putative regulatory roles for these largely uncharacterized genome components. Taken together, our integrative analyses reveal that epigenetic elements such as TEs, histone modifications and lncRNAs may have important roles in the acclimation of diatoms to elevated pCO2 over short time scales and thus may influence longer term adaptive processes in response to progressive ocean acidification.

microbiology↗

bioRxiv2018

Exosomes exploit the virus entry machinery and pathway to transmit IFN-α-induced antiviral activity.

Interferon- (IFN-) induces the transfer of resistance to hepatitis B virus (HBV) from liver nonparenchymal cells (LNPCs) to hepatocytes via exosomes. However, little is known about the entry machinery and pathway involved in the transmission of IFN--induced antiviral activity. Here, we found that macrophage exosomes depend on T cell immunoglobulin and mucin receptor 1 (TIM-1), a hepatitis A virus (HAV) receptor, to enter hepatocytes for delivering IFN--induced anti-HBV activity. Moreover, two primary endocytic routes for virus infection, clathrin-mediated endocytosis (CME) and macropinocytosis, collaborate to permit exosome entry and anti-HBV activity transfer. Subsequently, lysobisphosphatidic acid (LBPA), an anionic lipid closely related to endosome penetration of virus, facilitates membrane fusion of exosomes in late endosomes/ multivesicular bodies (LEs/MVBs) and the accompanying exosomal cargo uncoating. Together, this study provides comprehensive insights into the transmission route of macrophage exosomes to efficiently deliver IFN--induced anti-HBV activity and highlights the similarities between the entry mechanisms of exosomes and virus.\n\nImportanceOur previous study showed that LNPC-derived exosomes could transmit IFN--induced antiviral activity to HBV replicating hepatocytes, but the concrete transmission mechanisms which include exosome entry and exosomal cargo release remain unclear. In this study, we found that virus entry machinery and pathway were also applied to exosome-mediated cell-to-cell antiviral activity transfer. Macrophage-derived exosomes exploit hepatitis A virus receptor for access to hepatocytes. Later, CME and macropinocytosis are utilized by exosomes which is followed by exosome-endosome fusion for efficient transfer of IFN--induced anti-HBV activity. Dissecting the similarities between exosome and virus entry will be beneficial to designing exosomes as efficient vehicles for antiviral therapy.

microbiology↗

bioRxiv2018

Human noise blindness drives suboptimal cognitive inference

Humans typically make near-optimal sensorimotor judgments but show systematic biases when making more cognitive judgments. Here we test the hypothesis that, while humans are sensitive to the noise present during early sensory processing, the \"optimality gap\" arises because they are blind to noise introduced by later cognitive integration of variable or discordant pieces of information. In six psychophysical experiments, human observers judged the average orientation of an array of contrast gratings. We varied the stimulus contrast (encoding noise) and orientation variability (integration noise) of the array. Participants adapted near-optimally to changes in encoding noise, but, under increased integration noise, displayed a range of suboptimal behaviours: they ignored stimulus base rates, reported excessive confidence in their choices, and refrained from opting out of objectively difficult trials. These overconfident behaviours were captured by a Bayesian model which is blind to integration noise. Our study provides a computationally grounded explanation of suboptimal cognitive inferences.

neuroscience↗

bioRxiv2017

Cardiac directed differentiation using small molecule Wnt modulation at single-cell resolution

Differentiation into diverse cell lineages requires the orchestration of gene regulatory networks guiding diverse cell fate choices. Utilizing human pluripotent stem cells, we measured expression dynamics of 17,718 genes from 43,168 cells across five time points over a thirty day time-course of in vitro cardiac-directed differentiation. Unsupervised clustering and lineage prediction algorithms were used to map fate choices and transcriptional networks underlying cardiac differentiation. We leveraged this resource to identify strategies for controlling in vitro differentiation as it occurs in vivo. HOPX, a non-DNA binding homeodomain protein essential for heart development in vivo was identified as dys-regulated in in vitro derived cardiomyocytes. Utilizing genetic gain and loss of function approaches, we dissect the transcriptional complexity of the HOPX locus and identify the requirement of hypertrophic signaling for HOPX transcription in hPSC-derived cardiomyocytes. This work provides a single cell dissection of the transcriptional landscape of cardiac differentiation for broad applications of stem cells in cardiovascular biology.

developmental biology↗

bioRxiv2017

Genetic analysis of over one million people identifies 535 novel loci for blood pressure.

High blood pressure is the foremost heritable global risk factor for cardiovascular disease. We report the largest genetic association study of blood pressure traits to date (systolic, diastolic, pulse pressure) in over one million people of European ancestry. We identify 535 novel blood pressure loci that not only offer new biological insights into blood pressure regulation but also reveal shared loci influencing lifestyle exposures. Our findings offer the potential for a precision medicine strategy for future cardiovascular disease prevention.

genetics↗

bioRxiv2017

Interpretable dimensionality reduction of single cell transcriptome data with deep generative models

Single-cell RNA-sequencing has great potential to discover cell types, identify cell states, trace development lineages, and reconstruct the spatial organization of cells. However, dimension reduction to interpret structure in single-cell sequencing data remains a challenge. Existing algorithms are either not able to uncover the clustering structures in the data, or lose global information such as groups of clusters that are close to each other. We present a robust statistical model, scvis, to capture and visualize the low-dimensional structures in single-cell gene expression data. Simulation results demonstrate that low-dimensional representations learned by scvis preserve both the local and global neighbour structures in the data. In addition, scvis is robust to the number of data points and learns a probabilistic parametric mapping function to add new data points to an existing embedding. We then use scvis to analyze four single-cell RNA-sequencing datasets, exemplifying interpretable two-dimensional representations of the high-dimensional single-cell RNA-sequencing data.

bioinformatics↗

bioRxiv2017

Natural variation at FLOWERING LOCUS T2 mediates local adaptation in a key life history trait in European aspen

BackgroundThe initiation of growth cessation and dormancy represent critical life-history tradeoffs between survival and growth, and have important fitness effects in perennial plants. Such adaptive life history traits often show strong local adaptation along environmental gradients but despite their importance, the genetic architecture of these traits remains poorly understood.\n\nResultsWe integrate whole genome re-sequencing with environmental and phenotypic data from common garden experiments to investigate the genomic basis of local adaptation across a latitudinal gradient in European aspen (Populus tremula). We discover a single genomic region containing the PtFT2 gene that mediates local adaptation in the timing of bud set and that explains 65% of the observed genetic variation in bud set. This locus is the likely target of a recent selective sweep that originated right before or during colonization of northern Scandinavia following the last glaciation. Field and greenhouse experiments confirm that variation in PtFT2 gene expression affect the phenotypic variation in bud set that we observe in wild natural populations.\n\nConclusionsOur results reveal a major effect locus that determine the timing of bud set and that have facilitated rapid adaptation to shorter growing seasons and colder climates in European aspen. The discovery of a single locus explaining a substantial fraction of the variation in a key life history trait is remarkable given that such traits are generally considered to be highly polygenic. These findings provide a dramatic illustration of how loci of large-effect for adaptive traits can arise and be maintained over large geographical scales in natural populations.

evolutionary biology↗