Biology subjects

Song, Y.

Publications and source records attributed to Song, Y..

At least 379 records · Page 21Linked to original sources

bioRxiv2019

Inhibiting Mycobacterium tuberculosis ClpP1P2 by addressing the equatorial handle domain of ClpP1 subunit

Unlike other bacterial ClpP systems, mycobacterial ClpP1P2 complex is essential for mycobacterial survival. The functional details of Mycobacterium tuberculosis (Mtb) ClpP1P2 remains largely elusive and selectively targeting ClpP of different species is a big challenge. In this work, cediranib was demonstrated to significantly decrease the activity of MtbClpP1P2. By solving the crystal structure of cediranib-bound MtbClpP1P2, we found that cediranib dysregulates MtbClpP1P2 by interfering with handle domain of the equatorial region of MtbClpP1, indicating that the inter-ring dynamics are crucial for its function. This finding provides direct evidence for the notion that a conformational switch in the equatorial handle domain is essential for ClpP activity. We also present biochemical data to interpret the distinct interaction pattern and inhibitory properties of cediranib toward MtbClpP1P2. These results suggest that the variable handle domain region is responsible for the species-selectivity of cediranib, which suggests the equatorial handle domain as a potential region for screening pathogen-specific ClpP inhibitors.

biochemistry↗

bioRxiv2019

Single-cell entropy to quantify the cellular transcriptome from single-cell RNA-seq data

We present the use of single-cell entropy (scEntropy) to measure the order of the cellular transcriptome profile from single-cell RNA-seq data, which leads to a method of unsupervised cell type classification through scEntropy followed by the Gaussian mixture model (scEGMM). scEntropy is straightforward in defining an intrinsic transcriptional state of a cell. scEGMM is a coherent method of cell type classification that includes no parameters and no clustering; however, it is comparable to existing machine learning-based methods in benchmarking studies and facilitates biological interpretation.

bioinformatics↗

bioRxiv2019

Complete single neuron reconstruction reveals morphological diversity in molecularly defined claustral and cortical neuron types

Ever since the seminal findings of Ramon y Cajal, dendritic and axonal morphology has been recognized as a defining feature of neuronal types. Yet our knowledge concerning the diversity of neuronal morphologies, in particular distal axonal projection patterns, is extremely limited. To systematically obtain single neuron full morphology on a brain-wide scale, we established a platform with five major components: sparse labeling, whole-brain imaging, reconstruction, registration, and classification. We achieved sparse, robust and consistent fluorescent labeling of a wide range of neuronal types by combining transgenic or viral Cre delivery with novel transgenic reporter lines. We acquired high-resolution whole-brain fluorescent images from a large set of sparsely labeled brains using fluorescence micro-optical sectioning tomography (fMOST). We developed a set of software tools for efficient large-volume image data processing, registration to the Allen Mouse Brain Common Coordinate Framework (CCF), and computer-assisted morphological reconstruction. We reconstructed and analyzed the complete morphologies of 1,708 neurons from the striatum, thalamus, cortex and claustrum. Finally, we classified these cells into multiple morphological and projection types and identified a set of region-specific organizational rules of long-range axonal projections at the single cell level. Specifically, different neuron types from different regions follow highly distinct rules in convergent or divergent projection, feedforward or feedback axon termination patterns, and between-cell homogeneity or heterogeneity. Major molecularly defined classes or types of neurons have correspondingly distinct morphological and projection patterns, however, we also identify further remarkably extensive morphological and projection diversity at more fine-grained levels within the major types that cannot presently be accounted for by preexisting transcriptomic subtypes. These insights reinforce the importance of full morphological characterization of brain cell types and suggest a plethora of ways different cell types and individual neurons may contribute to the function of their respective circuits.

neuroscience↗

bioRxiv2019

The transcription factor Shox2 shapes thalamocortical neuron firing properties by regulation of key ion channels

Thalamocortical neurons (TCNs) transmit information about sensory stimuli from the thalamus to the cortex. In response to different physiological states and demands TCNs can fire in tonic and/or phasic burst modes. These firing properties of TCNs are supported by precisely timed inhibitory synaptic inputs from the thalamic reticular nucleus and intrinsic currents, including T-type Ca2+ and HCN currents. These intrinsic currents are mediated by Cav3.1 and HCN channel subunits, and alterations in expression or modulation of these channels can have dramatic implications on thalamus function. The factors that regulate these currents controlling the firing patterns important for integration of the sensory stimuli and the consequences resulting from the disruption of these firing patterns are not well understood. Shox2 is a transcription factor known to be important for pacemaker activity in the heart. We show here that Shox2 is also expressed in adult mouse thalamus. We hypothesized that genes regulated by Shox2s transcriptional activity may be important for physiological properties of TCNs. In this study, we used RNA sequencing on control and Shox2 knockout mice to determine Shox2-affected genes and revealed a network of ion channel genes important for neuronal firing properties. Quantitative PCR confirmed that expression of Hcn2, 4 and Cav3.1 genes were affected by Shox2 KO. Western blotting showed expression of the proteins for these channels was decreased in the thalamus, and electrophysiological recordings showed that Shox2 KO impacted the firing and synaptic properties of TCNs. Finally, behavioral studies revealed that Shox2 expression in TCNs play a role in somatosensory function and object recognition memory. Overall, these results reveal Shox2 as a transcription factor important for TCN firing properties and thalamic function.

neuroscience↗

bioRxiv2019

Highly precise base editing with CC context-specificity using engineered human APOBEC3G-nCas9 fusions

Cytidine base editors, composed of a cytidine deaminase fused to Cas9 nickase, enable efficient C-to-T conversion in various organisms. However, current base editors can induce unwanted bystander C-to-T conversions when more than one C is present in the activity window of cytidine deaminase, which negatively affects the precision. Here, we develop a new base editor with CC context-specificity using rationally engineered human APOBEC3G, thus significantly reduce unwanted bystander activities. In addition, efficient C-to-T conversion that can further recognize relaxed NG PAMs is achieved by combining an engineered SpCas9-NG variant. These novel base editors with improved precision and targeting scope will expand the toolset for precise gene modification in organisms.

molecular biology↗

bioRxiv2019

Modulation of emotion perception and memory via sub-threshold amygdala stimulation in humans

A common human experience is noticing that emotional life events are more vividly remembered than dull ones. Studies show that the amygdala plays a central role in such emotionally driven enhancement of memory. With this in mind, we investigated the effect of electrical brain stimulation of the left human amygdala on performance on an emotional perception and emotional memory task. We randomly applied sub-threshold 50 Hz stimulation to the left amygdala in 10 patients (5 female and 5 male) with intracranial electrodes during the encoding portion of an emotional valence perception and emotional memory task. We found that amygdala stimulation did not affect reported valence for neutral stimuli (non-stimulated group average valence 5.34, stimulated 5.38, p=0.68) but it did affect positively (non-stimulated group average valence 7.31, stimulated 6.70, p=0.004) and negatively (non-stimulated group average valence 2.79, stimulated 3.55, p=0.0002) valenced stimuli in effect reporting both valence categories as more neutral. Furthermore, we found that stimulation did not significantly disrupt memory for neutral stimuli (68% vs. 61% correctly remembered p=0.48) or positive stimuli (87% vs. 70% correct, trend towards significant difference p=0.09) but did for negative stimuli (83% vs. 67% correct, p=0.03). These results suggest that electrical brain stimulation by our parameters likely reversibly inhibits amygdala function disrupting neural networks responsible for emotional perception and memory. This effect may have clinical implications in treatment of certain neuropsychiatric disorders, such as emotional dysregulation and post-traumatic stress disorder.\n\nStatement of significanceThe current study builds and expands on extensive prior research into the function of the human amygdala. It provides the first systematic description in humans of a cognitive change brought about by direct electrical stimulation of the amygdala on perception of emotional valence and emotional memory. The results provide further evidence on the importance of the amygdala in human cognition. Likewise, out method utilized to study the function of the amygdala can be extended to study the function of other brain regions in humans, such as the cingulate. While these results are preliminary and need to be duplicated, we aim to further study the effects of amygdala stimulation on emotional processing including possible therapeutic application for diverse group of neuropsychiatric conditions.

neuroscience↗

bioRxiv2019

Individual differences in stereotypy and neuron subtype translatome with TrkB deletion

Motor stereotypies occurring in early-onset neuropsychiatric diseases are associated with dysregulated basal ganglia direct-pathway activity. Disruptions in network connectivity through impaired neuronal structure have been implicated in both rodents and humans. However, the neurobiological mechanisms leading to direct-pathway neuron disconnectivity in stereotypy remain poorly understood. We have a mouse line with Tropomyosin receptor kinase B (TrkB) receptor deletion from D1-expressing cells (D1-Cre-flTrkB) in which a subset of animals shows repetitive rotations and head tics with juvenile onset. Here we demonstrate these behaviors may be associated with abnormal direct-pathway activity by reducing rotations using chemogenetic inhibition of dorsal striatum D1-medium spiny neurons (D1-MSNs) in both juvenile and young adult mice. Taking advantage of phenotypical differences in animals with similar genotype, we then interrogated the D1-MSN specific translatome associated with repetitive behavior by using RNA-sequencing of ribosome-associated mRNA. Detailed translatome analysis followed by multiplexed gene expression assessment revealed profound alterations in neuronal projection and synaptic structure related genes in stereotypy mice. Examination of neuronal morphology demonstrated dendritic atrophy and dendritic spine loss in dorsal striatum D1-MSNs from mice with repetitive behavior. Together, our results uncover phenotype-specific molecular alterations in D1-MSNs that relate to morphological adaptations in mice displaying stereotypy behavior.

neuroscience↗

bioRxiv2019

Sequencing and comparative analysis of three Chlorella genomes provide insights into strain-specific adaptation to wastewater

Microalgal Chlorella has been demonstrated to process wastewater efficiently from piggery industry, yet optimization through genetic engineering of such a bio-treatment is currently challenging, largely due to the limited data and knowledge in genomics. In this study, we first investigated the differential growth rates among three wastewater-processing Chlorella strains: Chlorella sorokiniana BD09, Chlorella sorokiniana BD08 and Chlorella sp. Dachan, and the previously published Chlorella sorokiniana UTEX 1602, showing us that BD09 maintains the best tolerance in synthetic wastewater. We then performed genome sequencing and analysis, resulting in a high-quality assembly for each genome with scaffold N50 >2 Mb and genomic completeness [≥] 91%, as well as genome annotation with 9,668, 10,240, 9,821 high-confidence gene models predicted for BD09, BD08, and Dachan, respectively. Comparative genomics study unravels that metabolic pathways, which are involved in nitrogen and phosphorus assimilation, were enriched in the faster-growing strains. We found that gene structural variation and genomic rearrangement might contribute to differential capabilities in wastewater tolerance among the strains, as indicated by gene copy number variation, domain reshuffling of orthologs involved, as well as a [~]1 Mb-length chromosomal inversion we observed in BD08 and Dachan. In addition, we speculated that an associated bacterium, Microbacterium chocolatum, which was identified within Dachan, play a possible role in synergizing nutrient removal. Our three newly sequenced Chlorella genomes provide a fundamental foundation to understand the molecular basis of abiotic stress tolerance in wastewater treatment, which is essential for future genetic engineering and strain improvement.

genomics↗

bioRxiv2019

Multi-trait genome-wide association meta-analysis of dietary intake identifies new loci and genetic and functional links with metabolic traits

Dietary intake, a major contributor to the global obesity epidemic1-5, is a complex phenotype partially affected by innate physiological processes.6-11 However, previous genome-wide association studies (GWAS) have only implicated a few loci in variability of dietary composition.12-14 Here, we present a multi-trait genome-wide association meta-analysis of inter-individual variation in dietary intake in 283,119 European-ancestry participants from UK Biobank and CHARGE consortium, and identify 96 genome-wide significant loci. Dietary intake signals map to different brain tissues and are enriched for genes expressed in {beta}1-tanycytes and serotonergic and GABAergic neurons. We also find enrichment of biological pathways related to neurogenesis. Integration of cell-line and brain-specific epigenomic annotations identify 15 additional loci. Clustering of genome-wide significant variants yields three main genetic clusters with distinct associations with obesity and type 2 diabetes (T2D). Overall, these results enhance biological understanding of dietary composition, highlight neural mechanisms, and support functional follow-up experiments.

genetics↗

bioRxiv2019

A Genetically Encoded Fluorescent Sensor Enables Real-time Detection of the Intracellular GTP:GDP Ratio

The interconversion of guanosine triphosphate (GTP) and guanosine diphosphate (GDP) is integral to a wide variety of biological cellular activities. However, analytical methods which directly detect the ratio of intracellular GTP and GDP concentrations have not been available. Herein, we report GNEPS, a genetically encoded fluorescent sensor that enables real-time monitoring of the GTP:GDP ratio, which is a fusion protein comprising a eukaryotic G-protein and a circularly permuted yellow fluorescent protein. GNEPS has distinct fluorescence spectra between its GTP-bound and GDP-bound states. Its apparent fluorescence signal therefore depends upon the competitive binding of GTP and GDP. Live cell imaging experiments demonstrated that GNEPS can be used to monitor spatiotemporal changes in the intracellular GTP:GDP ratio in various cell types and organelles in response to metabolic perturbations. We anticipate that GNEPS will become a valuable tool for understanding the metabolic and regulatory contributions of guanosine nucleotides.

biochemistry↗

bioRxiv2019

Nanoscale subcellular architecture revealed by multicolor 3D salvaged fluorescence imaging

Combining the molecular specificity of fluorescent probes with three-dimensional (3D) imaging at nanoscale resolution is critical for investigating the spatial organization and interactions of cellular organelles and protein complexes. We present a super-resolution light microscope that enables simultaneous multicolor imaging of whole mammalian cells at ~20 nm 3D resolution. We show its power for cell biology research with fluorescence images that resolved the highly convoluted Golgi apparatus and the close contacts between the endoplasmic reticulum and the plasma membrane, structures that have traditionally been the imaging realm of electron microscopy.\n\nOne Sentence SummaryComplex cellular structures previously only resolved by electron microscopy can now be imaged in multiple colors by 4Pi-SMS.

biophysics↗

bioRxiv2019

Dynamic chromosome rearrangements of the white-spotted bamboo shark shed light on cartilaginous fish diversification mechanisms

Cartilaginous fishes have a very high phenotypical diversity, a phenomenon for which the mechanisms have been largely unexplored. Here, we report the genome of the white-spotted bamboo shark as the first chromosome-level genome assembly of cartilaginous fish. Using this genome, we illustrated a dynamic chromosome rearrangement process in the bamboo shark, which resulted in the formation of 13 chromosomes, all of which were sparsely distributed with conserved genes and fast-evolving. We found the fast-evolving chromosomes to be enriched in immune-related genes with two chromosomes harboring the major genes for developing the single-chain antibody. We also found chromosome rearrangements to have resulted in the loss of two genes (p2rx3 and p2rx5) which we also showed were involved in cartilage development using a CRISPR/Cas9 approach in zebrafish. Our study highlighted the significance of chromosome rearrangements in the phenotypical evolution of cartilaginous fishes, providing clues to inform further studies on mechanisms for fish diversification.

genomics↗

bioRxiv2019

Biological insights from multi-omic analysis of 31 genomic risk loci for adult hearing difficulty

Age-related hearing impairment (ARHI), one of the most common medical conditions, is strongly heritable, yet its genetic causes remain largely unknown. We conducted a meta-analysis of GWAS summary statistics from multiple hearing-related traits in the UK Biobank (n = up to 323,978) and identified 31 genome-wide significant risk loci for self-reported hearing difficulty (p < 5e-8), of which 30 have not been reported previously in the peer-reviewed literature at genome-wide significance. We investigated the regulatory and cell specific expression for these loci by generating mRNA-seq, ATAC-seq, and single-cell RNA-seq from cells in the mouse cochlea. Risk-associated genes were most strongly enriched for expression in cochlear epithelial cells, as well as for genes related to sensory perception and known Mendelian deafness genes, supporting their relevance to auditory function. Regions of the human genome homologous to open chromatin in sensory epithelial cells from the mouse were strongly enriched for heritable risk for hearing difficulty, even after adjusting for baseline effects of evolutionary conservation and cell-type nonspecific regulatory regions. Epigenomic and statistical fine-mapping most strongly supported 50 putative risk genes. Of these, at least 39 were expressed robustly in mouse cochlea and 16 were enriched specifically in sensory hair cells. These results reveal new risk loci and risk genes for hearing difficulty and suggest an important role for altered gene regulation in the cochlear sensory epithelium.

genetics↗

bioRxiv2019

A direct link between Prss53, hair curvature, and skeletal dysplasia

In humans, protease serine S1 family member 53 (Prss53) is highly expressed in the hair follicle, especially the inner root sheath, which is associated with hair shape according to recent genome-wide association study (GWAS) data. However, no animal evidence has indicated a link between Prss53 and hair shape to date. Here, we used CRISPR/Cas9 to generate Prss53-mutated rabbits. The homozygous (Prss53-/-) rabbits exhibited curved hair and skeletal dyskinesia with severe malformation, while the heterozygous (Prss53+/-) rabbits did not exhibit these features. The curvature features of the hair were accompanied by lesions that were generally denser and less well-defined in the cuticular septation of the hair shaft, and the compartments of the hair follicle were incomplete, as evidenced by decreased expression levels of keratinocyte differentiation genes. In addition, skeletal dysplasia, an increased lethality rate and decreased plasma calcium and serum alkaline phosphatase (ALP) levels were determined in the Prss53-/- rabbits. Furthermore, disrupted calcium metabolism, which may play a role in the hair curvature and skeletal dysplasia of Prss53+/- rabbits, was demonstrated by using high-throughput RNA sequencing data. Thus, our study confirmed for the first time that the loss of Prss53 lead to curved hair in animals and provides new insights into the crucial role of Prss53 in calcium metabolism. Author SummaryNo animal evidence has indicated a link between Prss53 and hair shape to date. The Prss53-/- rabbits exhibited curved hair and skeletal dyskinesia. The disrupted calcium metabolism may play a role in the hair curvature and skeletal dysplasia of Prss53+/- rabbits.

genomics↗

bioRxiv2019

Dengue and Zika virus 5′-UTRs harbor IRES functions

Members of Flavivirus, a genus of Flaviviridae, encompass numerous enveloped plus strand RNA viruses, of which globally dengue virus (DENV) is the leading cause of serious arthropod-borne disease. The genomes of DENV, just as those of yellow fever virus (YFV), West Nile fever virus (WNV), or Zika virus (ZIKV), control their translation by a 5-terminal capping group. Three other genera of Flaviviridae are remarkable because their viruses use internal ribosomal entry sites (IRESs) to control translation and they are not arthropod transmitted. In 2006 E. Harris group published work suggesting that DENV RNA does not stringently need a cap for translation. They proposed that instead DENV translation is controlled by an interplay between 5 and 3 termini. Here we present evidence that the DENV or ZIKV 5-untranslated regions (5-UTRs) alone have IRES competence. This conclusion is based, first, on the observation that uncapped mono-cistronic mRNAs 5 terminated with the DENV or ZIKV 5-UTRs can efficiently direct translation of a reporter gene in BHK and C6/36 cells; second, that either 5-UTR placed between two reporter genes can efficiently induce expression of the downstream gene in BHK but not in C6/36 cells. These experiments followed observations that uncapped DENV/ZIKV genomic transcripts, 5 terminated with pppAN... or GpppAN..., can initiate infections of mammalian (BHK) or mosquito (C6/36) cells. IRES competence of the 5-UTRs of DENV/ZIKV raises many open questions regarding the biology and control, as well as the evolution, of insect-borne flaviviruses. ImportanceMembers of the genus Flavivirus of Flaviviridae are important human pathogens of great concern because they cause serious diseases, sometimes death, in human populations living in tropical, subtropical (dengue, DENV; Zika, ZIKV; yellow fever virus), or moderate climates (West Nile virus). Flaviviruses are known to control their translation by a cap-dependent mechanism. We have observed, however, that the uncapped genomes of DENV or ZIKV can initiate infection of mammalian and insect cells. We provide evidence that the short 5 untranslated region (5-UTR) of DENV or ZIKV genomes can fulfill the function of an internal ribosomal entry site (IRES). This strategy frees these organisms from the cap-dependent mechanism of gene expression at an as yet unknown stage of proliferation. The data raise new questions about the biology and evolution of flaviviruses, possibly leading to new controls of flavivirus disease.

molecular biology↗

bioRxiv2019

Draft genome sequence of the Solanum aethiopicum provides insights into disease resistance, drought tolerance and the evolution of the genome

BackgroundS. aethiopicum is a close relative to S. melongena and has been routinely used to improve disease resistance in S. melongena. However, these efforts have been greatly limited by the lack of a reference genome and the clear understanding of the genes involved during biotic and abiotic stress response. ResultsWe present here a draft genome assembly of S. aethiopicum of 1.02 Gb in size, which is predominantly occupied by repetitive sequences (76.2%), particularly long terminal repeat elements. We annotated 37,681 gene models including 34,905 protein-coding genes. We observed an expansion of resistance genes through two rounds of amplification of LTR-Rs, occurred around 1.25 and 3.5 million years ago, respectively. The expansion also occurred in gene families related to drought tolerance. A number of 14,995,740 SNPs are identified by re-sequencing 65 S. aethiopicum genotypes including "Gilo" and "Shum" accessions, 41,046 of which are closely linked to resistance genes. The domestication and demographic history analysis reveals selection of genes involved in drought tolerance in both "Gilo" and "Shum" groups. A pan-genome of S. aethiopicum with a total of 36,250 protein-coding genes was assembled, of which 1,345 genes are missing in the reference genome. ConclusionsOverall, the genome sequence of S. aethiopicum increases our understanding of the genomic mechanisms of its extraordinary disease resistance and drought tolerance. The SNPs identified are available for potential use by breeders. The information provided here will greatly accelerate the selection and breeding of the African eggplant as well as other crops within the Solanaceae family.

genomics↗

bioRxiv2019

Bacterially produced spermidine induces plant systemic susceptibility to pathogens

Plant root-associated microbes promote plant growth and induce systemic resistance (ISR) to foliar pathogens. In an attempt to find novel growth-promoting and ISR-inducing strains, we previously identified strains of root-associated Pseudomonas spp. that promote plant growth but unexpectedly induced systemic susceptibility (ISS) rather than ISR to foliar pathogens. Here we demonstrate that the ISS-inducing phenotype is common among root-associated Pseudomonas spp. Using comparative genomics, we identified a single P. fluorescens locus that is unique to ISS strains. We generated a clean deletion of the 11-gene ISS locus and found that it is necessary for the ISS phenotype. Although the functions of the predicted genes in the locus are not apparent based on similarity to genes of known function, the ISS locus is present in diverse bacteria and a subset of the genes have previously been implicated in pathogenesis in animals. Collectively these data show that a single bacterial locus contributes to modulation of systemic plant immunity. ImportanceMicrobiome-associated bacteria can have diverse effects on health of their hosts, yet the genetic and molecular basis of these effects have largely remained elusive. This work demonstrates that a novel bacterial locus can modulate systemic plant immunity. Additionally, this work demonstrates that growth promoting strains may have unanticipated consequences on plant immunity and this is critical to consider when engineering the plant microbiome for agronomic improvement.

plant biology↗

bioRxiv2018

Deep-learning-based label-free segmentation of cell nuclei in time-lapse refractive index tomograms

In order to identify cell nuclei, fluorescent proteins or staining agents has been widely used. However, use of exogenous agents inevitably prevents from long-term imaging of live cells and rapid analysis, and even interferes with intrinsic physiological conditions. In this work, we proposed a method of label-free segmentation of cell nuclei in optical diffraction tomography images by exploiting a deep learning framework. The proposed method was applied for precise cell nucleus segmentation in two, three, and four-dimensional label-free imaging. A novel architecture with optimised training strategies was validated through cross-modality and cross-laboratory experiments. The proposed method would bring out broad and immediate biomedical applications with our framework publicly available.

biophysics↗