Biology subjects

Ding, J.

Publications and source records attributed to Ding, J..

At least 163 records · Page 9Linked to original sources

bioRxiv2021

Cellar: Interactive single cell data annotation tool

Several recent technologies and platforms enable the profiling of various molecular signals at the single-cell level. A key question for all studies using such data is the assignment of cell types. To improve the ability to correctly assign cell types in single and multi-omics sequencing and imaging single-cell studies, we developed Cellar. This interactive software tool supports all steps in the analysis and assignment process. We demonstrate the advantages of Cellar by using it to annotate several HuBMAP datasets from multi-omics single-cell sequencing and spatial proteomics studies. Cellar is freely available and includes several annotated reference HuBMAP datasets. Availabilityhttps://data.test.hubmapconsortium.org/app/cellar

bioinformatics↗

bioRxiv2021

New exon ignites accelerated evolution of placental gene Nrk in the ancestral lineage of eutherians

Accelerated evolution is often driven by the interaction between environmental factors and genes. However, it remains unclear whether accelerated evolution can be ignited. Here, we focused on adaptive events during the emergence of chorioallantoic placenta. We scanned the chromosome X and identified eight accelerated regions in the ancestral lineage of eutherian mammals. Five of these regions (P = 5.61 x 10-11 ~ 9.03 x 10-8) are located in the five exons of Nik-related kinase (Nrk), which is essential in placenta development and fetoplacental induction of labor. Moreover, a eutherian-specific exogenous exon lack of splice variant was found to be conserved. Structure modelling of NRK suggests that the accelerated exons and the eutherian-specific exon could change the enzymatic activity of eutherian NRK. Since the eutherian-specific exon was surrounded by accelerated exons, it indicates that the accelerated evolution of Nrk may be ignited by the emergence of the new exon in the ancestral lineage of eutherian mammals. The new exon might shift the function of Nrk and provide a new fitness landscape for eutherian species to explore. Although multiple exons were accelerated in both of the Nrk catalytic and regulatory domains, positive selection can only be revealed on the regulatory domain if the branch specific nonsynonymous and synonymous rate test was performed by PAML. Thus, it may be important to detect accelerated evolution when studying positive selection on coding regions. Overall, this work suggests that the fundamental process of placental development and fetoplacental induction of labor has been targeted by positive Darwinian selection. Identifying positively selected placental genes provides insights into how eutherian mammals gain benefits from the invasive chorioallantoic placenta to form one of the most successful groups among terrestrial vertebrates.

evolutionary biology↗

bioRxiv2021

Essential Role of Placenta Derived Interferon Stimulated Gene 20 Against ZIKA Virus Infection

Zika virus is a positive-sense single-stranded RNA virus, which can be transmitted across the placenta and leads to adverse effects on fetal development during pregnancy. The severity of these complications highlights the importance of prevention and treatment. However, no vaccines or drugs are currently available. In this study, we characterized the IFN{beta}-mediated antiviral response in trophoblast cells in order to identify critical components that are necessary for the successful control of viral replication; and determined whether we could use the components of the IFN-induced response as a replacement therapy for ZIKA viral infection during pregnancy. We identified and characterized interferon stimulated gene 20 (ISG20), playing a central role in controlling Zika infection in trophoblast cells, and successfully established a recombinant ISG20-Fc protein that effectively decrease viral titers in vitro and in vivo by maintaining its exonuclease activity and displaying immune modulatory functions. Therefore, rISG20-Fc is a promising anti-viral/immune modulatory approach for the control and prevention of RNA viral infections such as ZIKA virus.

immunology↗

bioRxiv2020

LISA: Learned Indexes for DNA Sequence Analysis

Next Generation Sequencing (NGS) is transforming fields like genomics, transcriptomics, and epigenetics with rapidly increasing throughput at reduced cost. This also demands overcoming performance bottlenecks in the downstream analysis of the sequencing data. A key performance bottleneck is searching for exact matches of entire or substrings of short DNA/RNA sequence queries in a long reference sequence database. This task is typically performed by using an index of the reference - such as FM-index, suffix arrays, suffix trees, hash tables, or lookup tables. In this paper, we propose accelerating this sequence search by substituting or enhancing the indexes with machine learning based indexes - called learned indexes - and present LISA (Learned Indexes for Sequence Analysis). We evaluate LISA through a number of case studies - that cover widely used software tools; short and long reads; human, animal, and plant genome datasets; DNA and RNA sequences; various traditional indexing techniques (FM-indexes, hash tables and suffix arrays) - and demonstrate significant performance benefits in a majority of them. For example, our experiments on real datasets show that LISA achieves speedups of up to 2.2 fold and 4.7 fold over the state-of-the-art FM-index based implementations for exact sequence search modules in popular tools bowtie2 and BWA-MEM2, respectively. Code availabilityLISA-based FM-index: https://github.com/IntelLabs/Trans-Omics-Acceleration-Library/tree/master/src/LISA-FMI LISA-based hash-table: https://github.com/IntelLabs/Trans-Omics-Acceleration-Library/tree/master/src/LISA-hash LISA applied to BWA-MEM2: https://github.com/bwa-mem2/bwa-mem2/tree/bwa-mem2-lisa.

bioinformatics↗

bioRxiv2020

Working Memory Capacities Neurally Dissociate: Evidence from Acute Stroke

Substantial behavioral evidence implies the existence of separable working memory (WM) components for maintaining phonological and semantic information. In contrast, only a few studies have addressed the neural basis of phonological vs. semantic WM using functional neuroimaging and none has used a lesion-symptom mapping (LSM) approach. Here we address this gap, reporting a multivariate LSM study of phonological and semantic WM for 94 individuals at the acute stage of left hemisphere stroke. Testing at the acute stage avoids issues of brain reorganization and the adoption of patient strategies for task performance. The LSM analyses for each WM component controlled for the other WM component and semantic and phonological knowledge at the single word level. For phonological WM, the regions uncovered included the supramarginal gyrus, argued to be the site of phonological storage, and several cortical and subcortical regions plausibly related to inner rehearsal. For semantic WM, inferior frontal regions and the angular gyrus were uncovered. The findings thus provide converging evidence for separable systems for phonological and semantic WM that are distinguished from the systems supporting long-term knowledge representations in those domains.

neuroscience↗

bioRxiv2020

Fast inactivation of Na+ current in rat adrenal chromaffin cells involves two independent inactivation pathways

Voltage-dependent sodium (Nav) current in adrenal chromaffin cells (CCs) is rapidly inactivating and TTX-sensitive. The fractional availability of CC Nav current has been implicated in regulation of action potential (AP) frequency and the occurrence of slow-wave burst firing. To ascertain whether features of CC Nav inactivation might influence AP firing, we recorded Nav current in rat CCs, primarily from adrenal medullary slices. A key feature of CC Nav current is that recovery from inactivation, even following brief (5 ms) inactivation steps, exhibits two exponential components of generally similar amplitude. Variations of standard paired pulse protocols support the view that entry into the fast and slower recovery processes result from largely independent, competing inactivation pathways, both of which occur with similar onset times at depolarizing potentials. Over voltages from -120 to -80 mV, faster recovery varies from ~3 to 30 ms, while slower recovery from about 50-400 ms. At strong activation voltages (+0 mV and more positive), the relative entry into slow or fast recovery pathways is similar and independent of voltage. Trains of brief inactivating steps result in cumulative increases in the slower recovery fraction. This supports idea that brief recovery intervals preferentially allow recovery of channels from fast recovery pathways, thereby increasing the fraction of channels in the slow recovery pathway with each subsequent inactivation step. This provides a mechanism whereby differential rates of recovery produce use-dependent accumulation in slower recovery pathways. Consistent with use-dependent accumulation of channels in slow recovery pathways, repetitive AP clamp waveforms at 1-10 Hz frequencies reduce Nav availability to 10-20% of initial amplitude dependent on holding potential. The results indicate that there are two distinct pathways of fast inactivation, one that leads to normal fast recovery and the other with a slower time course, which together are well-suited to mediate use-dependent changes in Nav availability.

biophysics↗

bioRxiv2020

Molecular and morphological analyses clarify species delimitation and reveal a new Betula species in section Costatae

Background and AimsDelineating closely related and morphologically similar species with overlapping ranges can be difficult. Here, we use section Costatae (genus Betula) as a model to resolve species and subspecies boundaries in four morphologically similar trees: Betula ashburneri, Betula costata, Betula ermanii and Betula utilis (including ssp. utilis, and diploid and tetraploid races of ssp. albosinensis). MethodsWe genotyped 298 individuals (20-80 per species) from 38 populations at 15 microsatellite markers and a subset of 34 individuals from 21 populations using restriction-site associated DNA sequencing (RAD-seq). Morphometric analysis was conducted to characterise leaf variation for a subset of 89 individuals. Key ResultsMolecular analyses and leaf morphology found little differentiation between B. ashburneri, diploid B. utilis ssp. albosinensis and some samples of B. utilis ssp. utilis suggesting that these should be treated as a single species. By contrast, tetraploid Betula utilis ssp. albosinensis was divided into two groups with group I genetically similar to B. utilis ssp. utilis based on SNPs and group II, a very distinct cluster, which we propose as a new species, namely, Betula buggsii. Phylogenomic analysis based on 2,285,620 SNPs show a well-supported monophyletic clade of B. buggsii, forming a sister with a well-supported clade of B. ashburneri, diploid B. albosinensis and some samples of B. utilis ssp. utilis. Morphologically, Betula buggsii is characterised by elongated lenticels and a distinct pattern of bark peeling. Betula buggsii is geographically restricted to the Qinling-Daba Mountains. ConclusionsOur study reveals six genetically distinguishable species: B. ashburneri, B. buggsii, B. costata, B. utilis ssp. utilis, B. utilis ssp. albosinensis and B. ermanii. Our research demonstrates an integrative approach in delimitating species using morphological and genetic samples from their nearly entire distributions. Analyses based on subsets of species distributions may lead to erroneous species or subspecies delineation.

evolutionary biology↗

bioRxiv2020

Multiple glacial refugia across northern and southern China and unexpected patterns of spatial genetic diversity in Betula albosinensis: a widespread temperate deciduous tree species

The central-marginal hypothesis (CMH) predicts high genetic diversity at the species geographic centre and low genetic diversity at the species geographic margins. However, most studies examining the CMH have neglected potential effect of past climate. Here, we test six hypotheses, representing effects of past climate and contemporary range position, for their ability to explain the spatial patterns of genetic diversity in 37 populations of Betula albosinensis. Ecological niche modelling (ENM) revealed large and continuous suitable habitats in north, southwest and southeast China during the last glacial maximum (LGM) but a contraction of suitable habitats since the LGM. Pollen records further confirmed the existence of multiple refugia in north and south China. The spatial pattern of genetic diversity (i.e., expected heterozygosity, gene diversity and allele richness) were best explained by distance to the southern edge and distance to the range edge but also showed longitudinal and latitudinal gradients. Hypotheses accounting for the effects of climate (climatic suitability, climatic stability and climatic variability) had comparatively little support. Our findings show partial support for the CMH and illustrates that the existence of multiple LGM refugia, and suggests species abundance and past species movement play a role in shaping genetic diversity across species ranges.

evolutionary biology↗

bioRxiv2020

Presence and Transmission of Mitochondrial Heteroplasmic Mutations in Human Populations of European and African Ancestry

We investigated the concordance of mitochondrial DNA heteroplasmic mutations (heteroplasmies) in different types of maternal pairs (n=6,745 pairs) of European (EA, n=4,718 pairs) and African (AA, n=2,027 pairs) Americans with whole genome sequences (WGSs). The average concordance rate of heteroplasmies was highest between mother-offspring pairs, followed by sibling-sibling pairs and more distantly related maternal pairs in both EA and AA participants. The allele fractions of concordant heteroplasmies exhibited high correlation (R2=0.8) between paired individuals. Compared to concordant heteroplasmies, discordant ones were more likely to locate in coding regions, be nonsynonymous or nonsynonymous-deleterious (p<0.001). The average number of heteroplasmies per individual (i.e. heteroplasmic burden) was at a similar level until older age (70-80 years old) and increased significantly thereafter (p<0.01). The burden of deleterious heteroplasmies (combined annotation-dependent depletion score[≥]15), however, was significantly correlated with advancing age (20-44, 45-64, [≥]65 years, p-trend=0.01). A genome-wide association analysis of the heteroplasmic burden identified many significant (P<5e-8) common variants (minor allele frequency>0.05) at 11p11.12. Many of the top SNPs act as strong long-range cis regulators of protein tyrosine phosphatase receptor type J. This study provides further evidence that mtDNA heteroplasmies may be inherited or somatic. Somatic heteroplasmic variants increase with advancing age and are more likely to have an adverse impact on mitochondrial function. Further studies are warranted for functional characterization of the deleterious heteroplasmies occurring with advancing age and the association of the 11p11.12 region of the nuclear genome with mtDNA heteroplasmy.

genetics↗

bioRxiv2020

A fluorescent sensor for spatiotemporally resolved endocannabinoid dynamics in vitro and in vivo

Endocannabinoids (eCBs) are retrograde neuromodulators that play an important role in a wide range of physiological processes; however, the release and in vivo dynamics of eCBs remain largely unknown, due in part to a lack of suitable probes capable of detecting eCBs with sufficient spatiotemporal resolution. Here, we developed a new eCB sensor called GRABeCB2.0. This genetically encoded sensor consists of the human CB1 cannabinoid receptor fused to circular-permutated EGFP, providing cell membrane trafficking, second-resolution kinetics, high specificity for eCBs, and a robust fluorescence response at physiological eCB concentrations. Using the GRABeCB2.0 sensor, we monitored evoked changes in eCB dynamics in both cultured neurons and acute brain slices. Interestingly, in cultured neurons we also observed spontaneous compartmental eCB transients that spanned a distance of approximately 11 m, suggesting constrained, localized eCB signaling. Moreover, by expressing GRABeCB2.0 in the mouse brain, we readily observed foot shock-elicited and running-triggered eCB transients in the basolateral amygdala and hippocampus, respectively. Lastly, we used GRABeCB2.0 in a mouse seizure model and observed a spreading wave of eCB release that followed a Ca2+ wave through the hippocampus. Thus, GRABeCB2.0 is a robust new probe for measuring the dynamics of eCB release under both physiological and pathological conditions.

neuroscience↗

bioRxiv2020

Identification of Lysine Isobutyrylation as A New Histone Modification Mark

Short-chain acylation of lysine residues in eukaryotic proteins are recognized as essential posttranslational chemical modifications (PTMs) that regulate cellular processes from transcription, cell cycle, metabolism, to signal transduction. Lysine butyrylation was initially discovered as a normal straight chain butyrylation (Knbu). Here we report its structural isomer, branched chain butyrylation, i.e. lysine isobutyrylation (Kibu), existing as a new PTM on nuclear histones. Uniquely, isobutyryl-CoA is derived from valine catabolism and branched chain fatty acid oxidation which is distinct from the metabolism of n-butyryl-CoA. Several histone acetyltransferases were found to possess lysine isobutyryltransferase activity, especially p300 and HAT1. We resolved the X-ray crystal structures of HAT1 in complex with isobutyryl-CoA that gleaned an atomic level insight into HAT-catalyzed isobutyrylation. RNA-Seq profiling revealed that isobutyrate greatly affected the expression of genes associated with many pivotal biological pathways. Our findings identify Kibu as a novel chemical modification mark in histones and suggest its extensive role in regulating epigenetics and cellular physiology.

biochemistry↗

bioRxiv2020

Targeting KRAS-mutant stomach/colorectal tumours by disrupting the ERK2-p53 complex

KRAS is widely mutated in human cancers, resulting in nearly unchecked tumour proliferation and metastasis. No therapies have been developed for targeting KRAS-mutant tumours. Herein, we observed that mutant KRAS specifically promoted the formation of ERK2-p53 complex in stomach/colorectal tumour cells. Disruption of this complex by applying MEK1/2 and ERK2 inhibitors elicits strong apoptotic responses in a p53-dependent manner, validated by genome-wide knockout screening. Mechanistically, p53 physically associates with phosphorylated ERK2 through the hydrophobic interaction in the presence of mutant KRAS, which suppresses p53 activation by preventing the recruitment of p300/CBP; trametinib disrupts the ERK2-p53 complex by reducing ERK2 phosphorylation, allowing the acetylation of p53 protein by recruiting p300/CBP; acetylated p53 activates PUMA transcription and thereby kills KRAS-mutant tumours. Our study unveils an important role of the ERK2-p53 complex and provides a potential therapeutic strategy for treating KRAS-mutant cancer via ERK2 inhibition.

cancer biology↗

bioRxiv2020

Identifying signaling genes in spatial single cell expression data

MotivationRecent technological advances enable the profiling of spatial single cell expression data. Such data presents a unique opportunity to study cell-cell interactions and the signaling genes that mediate them. However, most current methods for the analysis of this data focus on unsupervised descriptive modeling, making it hard to identify key signaling genes and quantitatively assess their impact. ResultsWe developed a Mixture of Experts for Spatial Signaling genes Identification (MESSI) method to identify active signaling genes within and between cells. The mixture of experts strategy enables MESSI to subdivide cells into subtypes. MESSI relies on multi-task learning using information from neighboring cells to improve the prediction of response genes within a cell. Applying the methods to three spatial single cell expression datasets, we show that MESSI accurately predicts the levels of response genes, improving upon prior methods and provides useful biological insights about key signaling genes and subtypes of excitatory neuron cells. AvailabilityMESSI is available at: https://github.com/doraadong/MESSI Contactzivbj@cs.cmu.edu

bioinformatics↗

bioRxiv2020

Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into the complex genetic architecture

The genetic basis of Lewy body dementia (LBD) is not well understood. Here, we performed whole-genome sequencing in large cohorts of LBD cases and neurologically healthy controls to study the genetic architecture of this understudied form of dementia and to generate a resource for the scientific community. Genome-wide association analysis identified five independent risk loci, whereas genome-wide gene-aggregation tests implicated mutations in the gene GBA. Genetic risk scores demonstrate that LBD shares risk profiles and pathways with Alzheimer’s and Parkinson’s disease, providing a deeper molecular understanding of the complex genetic architecture of this age-related neurodegenerative condition.Competing Interest StatementThomas G. Beach is a consultant for Prothena, Vivid Genomics and Avid Radiopharmaceuticals. He is a scientific advisory board member for Vivid Genomics. John A. Hardy, Huw R. Morris, Stuart Pickering-Brown, Andrew B. Singleton, and Bryan J. Traynor hold US, EU and Canadian patents on the clinical testing and therapeutic intervention for the hexanucleotide repeat expansion of C9orf72. Michael A. Nalls is supported by a consulting contract between Data Tecnica International and the National Institute on Aging, NIH, Bethesda, MD, USA; as a possible conflict of interest Dr. Nalls also consults for Neuron23 Inc., Lysosomal Therapeutics Inc., Illumina Inc., the Michael J. Fox Foundation and Vivid Genomics among others. Jose A. Palma is an editorial board member of Movement Disorders, Parkinsonism & Related Disorders, BMC Neurology, and Clinical Autonomic Research. Bradley F. Boeve, James Leverenz, and Sonja W. Scholz serve on the Scientific Advisory Council of the Lewy Body Dementia Association. Sonja W. Scholz is an editorial board member for the Journal of Parkinson's Disease. Bryan J. Traynor is an editorial board member for JAMA Neurology; Journal of Neurology, Neurosurgery, and Psychiatry; Brain; and Neurobiology of Aging. Zbigniew K. Wszolek serves as a principal investigator or co-principal investigator on Abbvie, Inc. (M15-562 and M15-563), Biogen, Inc. (228PD201) grant, and Biohaven Pharmaceuticals, Inc. (BHV4157-206 and BHV3241-301). Zbigniew K. Wszolek serves as the principal investigator of the Mayo Clinic American Parkinson Disease Association (APDA) Information and Referral Center, and as co-principal investigator of the Mayo Clinic APDA Center for Advanced Research. All other authors report no competing interests.View Full Text

genomics↗

bioRxiv2020

Structure and allosteric regulation of human IDH3 holoenzyme

Human NAD-dependent isocitrate dehydrogenase or IDH3 catalyzes the decarboxylation of isocitrate into -ketoglutarate in the TCA cycle. We here report the structure of the IDH3 holoenzyme, in which the {beta} and {gamma} heterodimers assemble the 2{beta}{gamma} heterotetramer via their clasp domains, and two 2{beta}{gamma} heterotetramers assemble the (2{beta}{gamma})2 heterooctamer via the {beta} and {gamma} subunits. The functional roles of the key residues involved in the assembly and allosteric regulation are validated by mutagenesis and kinetic studies. The allosteric site plays an important role but the pseudo allosteric site plays no role in the allosteric activation; the activation signal from the allosteric site is transmitted to the active sites of both heterodimers via the clasp domains; and the N-terminus of the {gamma} subunit plays a critical role in the formation and function of the holoenzyme. These findings reveal the molecular mechanism of the assembly and allosteric regulation of human IDH3 holoenzyme.

biochemistry↗

bioRxiv2020

Chromatin potential identified by shared single cell profiling of RNA and chromatin

Cell differentiation and function are regulated across multiple layers of gene regulation, including the modulation of gene expression by changes in chromatin accessibility. However, differentiation is an asynchronous process precluding a temporal understanding of the regulatory events leading to cell fate commitment. Here, we developed SHARE-seq, a highly scalable approach for measurement of chromatin accessibility and gene expression within the same single cell. Using 34,774 joint profiles from mouse skin, we develop a computational strategy to identify cis-regulatory interactions and define Domains of Regulatory Chromatin (DORCs), which significantly overlap with super-enhancers. We show that during lineage commitment, chromatin accessibility at DORCs precedes gene expression, suggesting changes in chromatin accessibility may prime cells for lineage commitment. We therefore develop a computational strategy (chromatin potential) to quantify chromatin lineage-priming and predict cell fate outcomes. Together, SHARE-seq provides an extensible platform to study regulatory circuitry across diverse cells within tissues.

genomics↗

bioRxiv2020

Bidirectional introgression between Betula tianshanica and Betula microphylla and its implications for conservation

O_LIMolecular markers can allow us to differentiate species that occupy a morphological continuum, and detect patterns of allele sharing that can help us understand the dynamics of geographic zones where they meet. Betula microphylla is a declining wetland species in NW China that forms a continuum of leaf morphology with its relative Betula tianshanica. C_LIO_LIWe use ecological niche models (ENM) to predict the distribution of B. microphylla, B. tianshanica and the more commonly occurring B. platyphylla. We use restriction-site associated DNA sequencing and SSRs to resolve their genetic structure and patterns of allele sharing. C_LIO_LIENM predicted an expansion of suitable range of B. tianshanica into B. microphylla since the Last Glacial Maximum and the contraction of B. microphyllas range in the future. We resolved the species identification of some intermediate morphotypes. We found signatures of bidirectional introgression between B. microphylla and B. tianshanica with SNPs showing more admixture than SSRs. Introgression from B. microphylla into B. tianshanica was greater in the Tianshan Mountains where the two species have occurred in proximity. Unexpectedly, introgression from B. tianshanica into B. microphylla was widespread in the Altay Mountains where there are no records of B. tianshanica occurrence. C_LIO_LIThis presence of B. tianshanica-derived alleles far beyond the species current range could be due to unexpectedly high pollen flow, undiscovered populations of B. tianshanica in the region, incomplete lineage sorting, or selection for adaptive introgression in B. microphylla. These different interpretations have contrasting implications for the conservation of B. microphylla. C_LI

evolutionary biology↗

bioRxiv2020

Reconstructing SARS-CoV-2 response signaling and regulatory networks

Several molecular datasets have been recently compiled to characterize the activity of SARS-CoV-2 within human cells. Here we extend computational methods to integrate several different types of sequence, functional and interaction data to reconstruct networks and pathways activated by the virus in host cells. We identify key proteins in these networks and further intersect them with genes differentially expressed at conditions that are known to impact viral activity. Several of the top ranked genes do not directly interact with virus proteins. We experimentally tested treatments for a number of the predicted targets. We show that blocking one of the predicted indirect targets significantly reduces viral loads in stem cell-derived alveolar epithelial type II cells (iAT2s). Software and interactive visualizationhttps://github.com/phoenixding/sdremsc

systems biology↗