Biology subjects

Zhao, J.

Publications and source records attributed to Zhao, J..

At least 559 records · Page 31Linked to original sources

bioRxiv2019

The dynamic transmission of positional information in stau- mutants during Drosophila embryogenesis

Intriguingly, the developmental patterning during Drosophila embryogenesis is highly accurate and robust despite its dynamic changes and constant fluctuations. It has been suggested that Staufen (Stau) is key in controlling the boundary variability of the gap protein Hunchback (Hb). However, its underlying mechanism is still elusive. Here, we have developed methods to quantify the dynamic 3D expression of segmentation genes in Drosophila embryos. With improved control of measurement errors, our results reveal that the posterior boundary of the Hb anterior domain (xHb) of stau- mutants shows comparable variability to that of the wild type (WT) and shifts posteriorly by nearly 12% of the embryo length (EL) to the WT position in the nuclear cycle (nc) 14. This observed large shift might contribute significantly to the apparent large variability of xHb in previous studies. Moreover, for stau- mutants, the upstream Bicoid (Bcd) gradients show equivalent gradient noise to that of the WT in nc12-nc14, and the downstream Even-skipped (Eve) and cephalic furrow (CF) show the same positional errors as the WT. Our results indicate that threshold-dependent activation and self-organized filtering are not mutually exclusive but could both be implemented in early Drosophila embryogenesis.

developmental biology↗

bioRxiv2019

FUNCTIONAL NETWORK CONNECTIVITY (FNC)-BASED GENERATIVE ADVERSARIAL NETWORK (GAN) AND ITS APPLICATIONS IN MENTAL DISORDERS DIAGNOSIS

Functional network connectivity (FNC) obtained from resting-state functional magnetic resonance imaging (fMRI) data have been commonly used to study mental disorders in neuroimaging applications. Likewise, generative adversarial networks (GANs) have performed well in multiple classification benchmark tasks. However, the application of GANs to fMRI is relatively rare. In this work, we proposed an FNC-based GAN for classifying brain disorders from healthy controls (HCs), in which FNC matrices were calculated by correlation of time courses derived from non-artefactual fMRI independent components (ICs). The proposed GAN model consisted of one discriminator (real FNCs) and one generator (fake FNCs), each has four fully-connected layers, and feature matching was implemented between each other to improve classification performance. An average accuracy of 70.1% with 10-fold cross-validation was achieved for classifying 269 major depressive disorder (MDD) patients from 286 HCs, at least 5.9% higher compared to other 6 popular classification approaches (54.5-64.2%). In another application to discriminating between 558 schizophrenia patients and 542 HCs from 7 sites, the proposed GAN model achieved 80.7% accuracy in leave-one-site-out prediction, outperforming support vector machine (SVM) and deep neural net (DNN) by 3-6%. To the best of our knowledge, this is the first attempt to apply GAN model based on fMRI data for mental disorder classification. Such a framework promises wide utility and great potential in neuroimaging biomarker identification.

bioengineering↗

bioRxiv2019

RNA G-quadruplex structures exist and function in vivo

Guanine-rich sequences are able to form complex RNA structures termed RNA G-quadruplexes in vitro. Because of their high stability, RNA G-quadruplexes are proposed to exist in vivo and are suggested to be associated with important biological relevance. However, there is a lack of direct evidence for RNA G-quadruplex formation in living cells. Therefore, it is unclear whether any purported functions are associated with the specific sequence content or the formation of an RNA G-quadruplex structure. Here, we profiled the landscape of those guanine-rich regions with the in vitro folding potential in the Arabidopsis transcriptome. We found a global enrichment of RNA G-quadruplexes with two G-quartets whereby the folding potential is strongly influenced by RNA secondary structures. Using in vitro and in vivo RNA chemical structure profiling, we determined that hundreds of RNA G-quadruplex structures are strongly folded in both Arabidopsis and rice, providing direct evidence of RNA G-quadruplex formation in living eukaryotic cells. Subsequent genetic and biochemical analysis showed that RNA G-quadruplex folding was sufficient to regulate translation and modulate plant growth. Our study reveals the existence of RNA G-quadruplex in vivo, and indicates that RNA G-quadruplex structures act as important regulators of plant development and growth.

plant biology↗

bioRxiv2019

Dissemination of linezolid-resistance through sex pheromone plasmid transfer in Enterococcs faecalis

Despite recent recognition of the ATP-binding cassette protein OptrA as an important mediator of linezolid-resistance in Enterococcus faecalis worldwide, the mechanisms of optrA gene acquisition and transfer remain poorly understood. In this study, we performed comprehensive molecular and phenotypic profiling of 44 optrA-carrying E. faecalis clinical isolates with linezolid-resistance. Pulse-field gel electrophoresis and DNA hybridization revealed the presence of optrA in the plasmid in 26 (59%) isolates and in the chromosome in 18 (41%) isolates. Conjugation experiments showed a successful transfer of optrA in 88.5% (23/26) of isolates carrying optrA in plasmids while no transfer occurred in any isolates carrying optrA in the chromosome (0/18). All 23 transconjugants exhibited in vitro resistance to linezolid and several other antibiotics, and were confirmed to contain optrA and other resistance genes. Plasmid typing demonstrated a predominance (18/23 or 78%) of rep9-type plasmids (pCF10 prototype) known to be the best studied sex pheromone responsive plasmids. Full plasmid genome sequencing of one isolate revealed the presence of drug resistance genes (optrA and fexA) and multiple sex pheromone response genes in the same plasmid, which represents the first sex pheromone responsive plasmid carrying optrA from a clinical isolate. PCR-based genotyping revealed the presence of three key sex pheromone response genes (prgA, prgB and prgC) in almost all 23 optrA-carrying isolates tested. Finally, functional studies of these isolates by clumping induction assay detected different degrees of clumping in most of the 23 isolates. Our analysis strongly suggests that optrA-mediated linezolid-resistance can be widely disseminated through sex pheromone plasmid transfer.

microbiology↗

bioRxiv2019

DNB-Based On-Chip Motif Finding (DocMF): a High-Throughput Method to Profile Different Types of Protein-DNA Interactions

Here we report a highly sensitive DNB-based on-chip Motif Finding (DocMF) system that utilizes high throughput next-generation-sequencing (NGS) chips to profile protein binding or cleaving activity. Using DocMF, we successfully identified a variety of endonuclease recognition sites and the protospacer-adjacent-motif (PAM) sequences of different CRISPR systems. Our DocMF platform can simultaneously screen both 5 and 3 PAM regions with high coverage using the same NGS library/chip. For the well-studied SpCas9, our DocMF platform identified a small proportion of noncanonical 5-NAG-3 ([~]5%) and 5-NGA-3 ([~]1.6%), in addition to its common PAMs, 5-NGG-3 ([~]89.9%). We also used the DocMF to assay two uncharacterized Cas endonucleases, VeCas9 and BvCpf1. VeCas9 PAMs were not detected by the conventional PAM depletion method. However, DocMF discovered that both VeCas9 and BvCpf1 required broader and more complicated PAM sequences for target recognition. VeCas9 preferred the R-rich motifs, whereas BvCpf1 used the T-rich PAMs. Moreover, after slightly changing the experimental protocol, we observed that dCas9, a DNA-binding protein lacking endonuclease activity, preferably binded to the previously reported PAMs 5-NGG-3. In summary, our studies demonstrate that DocMF is the first tool with the capacity to exhaustively assay both the binding and the cutting properties of different DNA-binding proteins.

molecular biology↗

bioRxiv2019

Glutamate-ammonia ligase promotes lung cancer cell growth through an enzyme independent upregulation of CaMK2G under a glutamine-sufficient condition

Glutamate-ammonia ligase (GLUL) is highly expressed in many cancer cells. Synthesizing glutamine by its enzyme function has been found to be important for supporting cancer cell survival and growth under glutamine restriction. However, GLULs functions under a glutamine-sufficient condition still have not been uncovered. Here we find that GLUL is highly expressed in lung cancer cells and provides survival and growth advantages under both glutamine restriction and adequacy conditions. Knocking down GLUL can block lung cancer cell growth in an enzyme-independent way when glutamine is sufficient. Mechanistically, GLUL regulates Calcium/Calmodulin Dependent Protein Kinase II Gamma (CaMK2G) expression at the transcription level, and CaMK2G is a major mediator in controlling cell growth under GLUL. The transcriptional regulation of CaMK2G is partially mediated by SMAD4. Our data unveil a new enzyme-independent function of GLUL in lung cancer cells under a glutamine-sufficient condition.

cancer biology↗

bioRxiv2019

Amino and PEG-Amino Graphene Oxide Grids Enrich and Protect Samples for High-resolution Single Particle Cryo-electron Microscopy

Cryo-EM samples prepared using the traditional methods often suffer from too few particles, poor particle distribution, or strongly biased orientation, or damage from the air-water interface. Here we report that functionalization of graphene oxide (GO) coated grids with amino groups concentrates samples on the grid with improved distribution and orientation. By introducing a PEG spacer, particles are kept away from both the GO surface and the air-water interface, protecting them from potential denaturation.

biophysics↗

bioRxiv2019

The Bovine Genome Variation Database (BGVD): Integrated Web-database for Bovine Sequencing Variations and Selective Signatures

Next-generation sequencing has yielded a vast amount of cattle genomic data for the global characterization of population genetic diversity and the identification of regions of the genome under natural and artificial selection. However, efficient storage, querying and visualization of such large datasets remain challenging. Here, we developed a comprehensive Bovine Genome Variation Database (BGVD, http://animal.nwsuaf.edu.cn/BosVar) that provides six main functionalities: Gene Search, Variation Search, Genomic Signature Search, Genome Browser, Alignment Search Tools and the Genome Coordinate Conversion Tool. The BGVD contains information on genomic variations comprising [~]60.44 M SNPs, [~]6.86 M indels, 76,634 CNV regions and signatures of selective sweeps in 432 samples from modern cattle worldwide. Users can quickly retrieve distribution patterns of these variations for 54 cattle breeds through an interactive source of breed origin map using a given gene symbol or genomic region for any of the three versions of the bovine reference genomes (ARS-UCD1.2, UMD3.1.1, and Btau 5.0.1). Signals of selection are displayed as Manhattan plots and Genome Browser tracks. To further investigate and visualize the relationships between variants and signatures of selection, the Genome Browser integrates all variations, selection data and resources from NCBI, the UCSC Genome Browser and AnimalQTLdb. Collectively, all these features make the BGVD a useful archive for in-depth data mining and analyses of cattle biology and cattle breeding on a global scale.

genomics↗

bioRxiv2019

Defining relative mutational difficulty to understand cancer formation and prevention

Most mutations in human cancer are low-frequency missense mutations, whose functional status remains hard to predict. Here we show that depending on the type of nucleotide change and the surrounding sequences, the tendency to generate each type of nucleotide mutations varies greatly, even by several hundred folds. Therefore, a cancer-promoting mutation may appear only in a small number of cancer cases, if the underlying nucleotide change is too difficult to generate. We propose a method that integrates both the original mutation counts and their relative mutational difficulty. Using this method, we can accurately predict the functionality of hundreds of low-frequency missense mutations in p53, PTEN and INK4A. Many loss-of-function p53 mutations with dominant negative effects were identified, and the functional importance of several regions in p53 structure were highlighted by this analysis. Furthermore, mutational difficulty analysis also points to potential means of cancer prevention. Our study not only established relative mutational difficulties for different types of mutations in human cancer, but also showed that by incorporating such parameter, we can bring new angles to understanding cancer formation and prevention.

cancer biology↗

bioRxiv2019

Causal inference for the effect of environmental chemicals on chronic kidney disease

There is evidence from a limited number of statistical and animal studies that suggest that perfluoroalkyl acids (PFAs) are linked to a decline in kidney function. Thus, PFA exposure may be a modifiable risk factor for chronic kidney disease (CKD). As PFA is pervasive throughout our environment, determining its health effects is an important public health concern. We examined cross-sectional data from the 2009-2010 cycle of NHANES using generalized propensity score (GPS) analysis and univariate and multivariate ordinary least squares (OLS) regression to determine the link between urinary PFA concentration and estimated glomerular filtration rate (eGFR). GPS estimation methods used were Hirano-Imbens, additive spline, and a generalized additive model. Each of the statistical models used associated an increase in PFA concentration with a decline in eGFR, though the eGFR fit using the multivariate regression model were consistently higher than from the other four models. We conclude that PFA is a modifiable risk factor for CKD and GPS analysis produces credible results in estimating the effect of chemical exposures on continuous measure of kidney functions such as eGFR.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC=\"FIGDIR/small/769430v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (13K):\norg.highwire.dtl.DTLVardef@19c1773org.highwire.dtl.DTLVardef@c79b8aorg.highwire.dtl.DTLVardef@b4b6c4org.highwire.dtl.DTLVardef@4b0253_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

bioinformatics↗

bioRxiv2019

γ-Secretase controls the specification of astrocytes from oligodendrocyte precursor cells via Stat3

Oligodendrocytes (OLs) and astrocytes play critical roles in a variety of brain functions. OL precursor cells (OPCs) are known to give rise to OLs as well as astrocytes. However, little is known about the mechanism by which OPCs determine their specification choice for OLs versus astrocytes in the central nervous system (CNS). Here we show that genetic inhibition of {gamma}-secretase in OPCs reduces OL differentiation but enhances astrocyte specification. Mechanistic analysis reveals that inhibition of {gamma}-secretase results in decreased levels of Hes1, and that Hes1 down-regulates the expression of signal transducer and activator of transcription3 (Stat3) via binding to specific regions of its promoter. We demonstrate that conditional inactivation of Stat3 in OL lineages restores the number of astrocytes in {gamma}-secretase mutant mice. In summary, this study identifies a key mechanism which controls OPCs specification choice for OL versus astrocyte during postnatal development. This {gamma}-secretase-dependent machinery may be essential for the CNS to maintain the population balance between OLs and astrocytes.

neuroscience↗

bioRxiv2019

Geomagnetic field absence influences adult body weight of a migratory insect, potentially through appetite regulation

The geomagnetic field (GMF) is well documented for its essential role as a cue used in animal orientation or navigation. Recent evidence indicates that the absence of GMF can trigger stress-like responses such as reduced body weight, as we have previously shown in newly emerged adults of the brown planthopper, Nilaparvata lugens. To test the hypothesis that reduced feeding in the absence of the GMF leads to a decrease of N. lugens body weight, we compared magnetic responses in feeding behavior, glucose levels, and expression of magnetoreception- and appetite-related genes in brown planthopper nymphs exposed to either a near-zero magnetic field (NZMF, i.e., GMF absence) or typical GMF conditions. In addition to observing the expected responses in the expression of the potential magnetosensor cryptochromes, the food intake of 5th instar nymphs was significantly reduced in insects reared in the absence of GMF. Insects that exhibited reduced feeding reared in the absence of the GMF also had higher glucose levels which is associated with food aversion. Expression patterns of appetite-related neuropeptide genes were also altered in the absence of GMF in a manner consistent with diminishing appetite. These findings support the hypothesis that strong changes in GMF intensity can affect insect feeding behavior and underlying regulatory processes. Our results provide further evidence that magnetoreception and regulatory responses to GMF changes can affect a wide variety of biological processes.

animal behavior and cognition↗

bioRxiv2019

The Structural Basis of Indisulam-Mediated Recruitment of RBM39 to the DCAF15-DDB1-DDA1 E3 Ligase Complex

The anti-cancer agent Indisulam inhibits cell proliferation by causing degradation of RBM39, an essential mRNA splicing factor. Indisulam promotes an interaction between RBM39 and the DCAF15 E3 ligase substrate receptor leading to RBM39 ubiquitination and proteasome-mediated degradation. To delineate the precise mechanism by which Indisulam mediates DCAF15-RBM39 interaction, we solved the DCAF15-DDB1-DDA1-Indisulam-RBM39(RRM2) complex structure to 2.3 [A]. DCAF15 has a novel topology which embraces the RBM39(RRM2) domain largely via nonpolar interactions, and Indisulam binds between DCAF15 and RBM39(RRM2) and coordinates additional interactions between the two proteins. Studies with RBM39 point mutants and Indisulam analogs validated the structural model and defined the RBM39 alpha-helical degron motif. The degron is found only in RBM23 and RBM39 and only these proteins were detectably downregulated in Indisulam-treated HCT116 cells. This work further explains how Indisulam induces RBM39 degradation and defines the challenge of harnessing DCAF15 to degrade novel targets.

biophysics↗

bioRxiv2019

Detecting regions of differential abundance betweenscRNA-Seq datasets

Traditional cell clustering analysis used to compare the transcriptomic landscapes between two biological states in single cell RNA sequencing (scRNA-seq) is largely inadequate to functionally identify distinct and important differentially abundant (DA) subpopulations between groups. This problem is exacerbated further when using unsupervised clustering approaches where differences are not observed in clear cluster structure and therefore many important differences between two biological states go entirely unseen. Here, we develop DA-seq, a powerful unbiased, multi-scale algorithm that uniquely detects and decodes novel DA subpopulations not restricted to well separated clusters or known cell types. We apply DA-seq to several publicly available scRNA-seq datasets on various biological systems to detect differences between distinct phenotype in COVID-19 cases, melanomas subjected to immune checkpoint therapy, embryonic development and aging brain, as well as simulated data. Importantly, we find that DA-seq not only recovers the DA cell types as discovered in the original studies, but also reveals new DA subpopulations that were not described before. Analysis of these novel subpopulations yields new biological insights that would otherwise be neglected.

bioinformatics↗

bioRxiv2019

Olaparib and Enzalutamide synergistically suppress HCC progression via the AR-mediated miR-146a-5p/BRCA1 signaling

Hepatocellular carcinoma (HCC) is one of most common malignant tumors worldwide, however, the treatment for advanced HCC remains unsatisfactory. Here we found that Olaparib, a FDA approved PARP inhibitor, could enhance the cytotoxicity in HCC cells with a lower BRCA1 expression, and suppressing the AR with either Enz or AR-shRNA could further increase the Olaparib sensitivity to better suppress the HCC cell growth via a synergistic mechanism that may involve suppressing the expression of BRCA1 and other DNA damage response (DDR) genes. Mechanism studies revealed that Enz/AR signaling might transcriptional regulting the miR-146a-5p expression via binding to the AREs on its 5 promoter region, which could then lead to suppress the homologous recombination-related BRCA1 expression via direct binding to its 3 UTR of mRNA. Preclinical study using an in vivo mouse model also proved that combined Enz plus Olaparib led to better suppression of the HCC progression. Together, these in vitro/in vivo data suggest that combining Enz and Olaparib may help in the development of a novel therapy to better suppress the HCC progression.

synthetic biology↗

bioRxiv2019

CD8+ T-cell-mediated immunoediting influences genomic evolution and immune evasion in murine gliomas

Cancer immunoediting shapes tumor progression by the selection of tumor cell variants that can evade immune recognition. Given the immune evasion and intra-tumor heterogeneity intrinsic to gliomas, we hypothesized that CD8+ T-cells mediate immunoediting in these tumors. We evaluated glioma progression in the absence of CD8+ T-cells by depleting this immune cell population in transgenic murine gliomas. Upon transplantation, gliomas that developed in the absence of CD8+ T-cells engrafted poorly in recipients with intact immunity but engrafted well in those with CD8+ T-cell depletion. Gliomas developed in absence of CD8+ T-cells exhibited increased chromosomal instability, MAPK signaling, gene fusions, and macrophage/microglial infiltration. MAPK activation correlated with macrophage/microglial recruitment in this model and in the human disease. Our results indicate that CD8+ T-cells mediate immunoediting during gliomagenesis, influencing the genomic stability of glioma and its microenvironment, leading to immune evasion.\n\nSignificanceImmune evasion renders cancer resistant to anti-tumoral immunity. Therapeutic intervention often fails for gliomas because of the plasticity of tumor cell variants that resist immune surveillance. Our results demonstrate a mechanism of immune evasion in gliomas that derives from CD8+ T-cells during the development and progression of this disease.

cancer biology↗

bioRxiv2019

Presynaptic Gαo (GOA-1) signaling depresses command neuron excitability to allow for stretch-dependent modulation of egg-laying behavior in C. elegans

Egg laying in the nematode worm Caenorhabditis elegans is a two-state behavior modulated by internal and external sensory input. We have previously shown that homeostatic feedback of embryo accumulation in the uterus regulates bursting activity of the serotonergic HSN command neurons that sustains the egg-laying active state. How sensory feedback of egg release signals to terminate the egg-laying active state is less understood. We find that Go, a conserved Pertussis Toxin-sensitive G protein, signals within HSN to inhibit egg-laying circuit activity and prevent entry into the active state. Go signaling hyperpolarizes HSN, reducing HSN Ca2+ activity and input onto the postsynaptic vulval muscles. Loss of inhibitory Go signaling uncouples presynaptic HSN activity from a postsynaptic, stretch-dependent homeostat, causing precocious entry into the egg-laying active state when only a few eggs are present in the uterus. Feedback of vulval opening and egg release activates the uv1 neuroendocrine cells which release NLP-7 neuropeptides which signal to inhibit egg laying through Go-independent mechanisms in the HSNs and Go-dependent mechanisms in cells other than the HSNs. Thus, neuropeptide and inhibitory Go signaling maintains a bi-stable state of electrical excitability that dynamically controls circuit activity in response to both external and internal sensory input to drive a two-state behavior output.

neuroscience↗

bioRxiv2019

Sub-nucleosomal organization in urine cell-free DNA

Cell-free DNA (cfDNA) in urine is a promising analyte for noninvasive diagnostics. However, urine cfDNA is highly fragmented and whether characteristics of these fragments reflect underlying genomic architecture is unknown. Here, we perform comprehensive characterization of fragmentation patterns in urine cfDNA. We show modal size and genome-wide distribution of urine cfDNA fragments are consistent with transient protection from degradation by stable intermediates of nucleosome disassembly. Genome-wide nucleosome occupancy and fragment sizes in urine cfDNA are informative of cell of origin and renal epithelial cells are amongst the highest contributors in urine. Compared to a nucleosome occupancy map based on control urine samples, we observe a higher fraction of fragments with aberrant ends in cancer patients, distinguishing cancer samples with an area under the curve of 0.89. Our results demonstrate sub-nucleosomal organization in urine cfDNA and are proof-of-principle that genome-wide fragmentation analysis of urine cfDNA can enable cancer diagnostics.

genomics↗