Biology subjects

Cao, J.

Publications and source records attributed to Cao, J..

211 records · Page 12Linked to original sources

bioRxiv2018

The Role of Gdf5 Regulatory Regions on Development of Hip Morphology and Susceptibility to Osteoarthritis and Dislocation

Given GDF5 involvement in hip development, and osteoarthritis (OA) and developmental hip dysplasia (DDH) risk, here we sought to assess the role(s) of GDF5 and its regulatory sequence on the development of hip morphology linked to injury risk. The brachypodism (bp) mouse, which harbors a Gdf5 inactivating mutation, was used to survey how Gdf5 loss of function impacts the development of hip morphology. Two transgenic Gdf5 reporter BAC lines were used to assess the spatiotemporal expression of Gdf5 regulatory sequences. Each BAC line was also used to assess the functional roles of upstream and downstream sequence on hip morphology. bp/bp mice had shorter femora with smaller femoral heads and necks as well as larger alpha angles, smaller anterior offsets, and smaller acetabula, compared to bp/+ mice (p<0.04). Regulatory sequences downstream of Gdf5 drove strong prenatal (E17) expression and low postnatal (6 months) expression across regions of femoral head and acetabulum. Conversely, upstream regulatory sequences drove very low expression at E17 and no detectable expression at 6 months. Importantly, downstream, but not upstream Gdf5 regulatory sequences fully restored all the key morphologic features disrupted in bp/bp mice. Hip morphology is profoundly affected by Gdf5 absence, and downstream regulatory sequences mediate its effects by controlling Gdf5 expression during development. This downstream region contains numerous enhancers harboring risk variants related to hip OA, DDH, and dislocation. We posit that subtle alterations to morphology driven by changes in downstream regulatory sequence underlie this locus role in hip injury risk.

genetics↗

bioRxiv2018

Effects of different pretreatments on flavonoids and antioxidant activity of Dryopteris erythrosora leave

Flavonoids with wide bioactivity for medcine are vital secondary metabolite of plant. The factors influenced on flavonoids had been reported. However, as the key processes lead to metabolite alterations, the influences of the different pretreatments of samples on flavonoids and antioxidant activity of ferns were with little information. Therefore, Dryopteris erythrosora leaves were chosen as the materials for analyzing flavonoids alterations, which would not only provide the significant basic data for flavonoid metabolism of fern, but also for further developing fern resources. The results showed that a) The total flavonoids contents of D. erythrosora leaves with different pretreatments were obviously different. The total flavonoid contents of samples, which was dried in shade firstly and then dried at 75 {degrees}C in oven, finally smashed, was the highest (7.6%), but that of samples, which was quickly dried at 75 {degrees}C in oven directly after cleaning and then smashed, was the lowest (2.17%); b) Antioxidant activities of D. erythrosora leaves with different pretreatments were variant. Samples, which were dried in shade firstly and then dried at 75 {degrees}C in oven, finally smashed and samples which were firstly dried in the sun and then dried at 75 {degrees}C in oven, ultimately smashed, both showed stronger antioxidant activity; c) Total twenty-three flavonoids with four different pretreatments were tentatively identified by HPLC-ESI-TOF-MS. In conlusion, a) The influences of different pretreatments on flavonoids and antioxidant activity of D. erythrosora Leaves were obvious. b) The best pretreatment in respect to conserving fern medical application was drying in shade firstly and then drying at 75 {degrees}C in oven, finally smashed.

plant biology↗

bioRxiv2018

Identification and Characterisation of the CD40-Ligand of Sigmodon hispidus

Cotton rats are an important animal model to study infectious diseases. They have demonstrated higher susceptibility to a wider variety of human pathogens than other rodents and are also the animal model of choice for pre-clinical evaluations of some vaccine candidates. However, the genome of cotton rats remains to be fully sequenced, with much fewer genes cloned and characterised compared to other rodent species. Here we report the cloning and characterization of CD40 ligand, whose human and murine counterparts are known to be expressed on a range of cell types including activated T cells and B cells, dendritic cells, granulocytes, macrophages and platelets and exerts a broad array of immune responses. The cDNA for cotton rat CD40L we isolated is comprised of 1104 nucleotides with an open reading frame (ORF) of 783bp coding for a 260 amino acid protein. The recombinant cotton rat CD40L protein was recognized by an antibody against mouse CD40L. Moreover, it demonstrated functional activities on immature bone marrow dendritic cells by upregulating surface maturation markers (CD40, CD54, CD80, and CD86), and increasing IL-6 gene and protein expression. The availability of CD40L gene identity could greatly facilitate mechanistic research on pathogen-induced-immunopathogenesis and vaccine-elicited immune responses.

immunology↗

bioRxiv2018

The variability of amino acids sequences in hepatitis B virus

Hepatitis B virus (HBV) is an important human pathogen belonging to the Hepadnaviridae family, Orthohepadnavirus genus. It infects over 240 million people globally. The reverse transcription during its genome replication leads to low fidelity DNA synthesis, which is the source of variability in the viral proteins. To investigate the variability quantitatively, we retrieved amino acid sequences of 5167 records of all available HBV genotypes (A-J) from the Genbank database. The amino acid sequences encoded by the open reading frames (ORF) S/C/P/X in the HBV genome were extracted and subjected to alignment respectively. We analyzed the variability of the lengths and the sequences of proteins as well as the frequencies of amino acids. Our study comprehensively characterized of the variability and conservation of HBV at the level of amino acids, especially for the structural proteins, hepatitis B surface antigens (HBsAg), to find out the potential sites critical for virus assembly and immune recognition. Interestingly, the preS1/S2 domains in HBsAg were variable at some positions of amino acid residues, which provides a potential mechanism of immune-escape for HBV, while the preS2 and S domains were conserved in the lengths of protein sequences. In the S domain, the cysteine residues and the secondary structures of the alpha-helix and beta-sheet were likely critical for the stable folding of the protein structure. The preC domain and C-terminal domain (CTD) of the core protein are highly conserved. And the polymerases HBpol and the HBx were highly variable at the amino acid level.

microbiology↗

bioRxiv2018

Characterization and identification of long non-coding RNAs based on feature relationship

The significance of long non-coding RNAs (lncRNAs) in many biological processes and diseases has gained intense interests over the past several years. However, computational identification of lncRNAs in a wide range of species remains challenging; it requires prior knowledge of well-established sequences and annotations or species-specific training data, but the reality is that only a limited number of species have high-quality sequences and annotations. Here we first characterize lncRNAs by contrast to protein-coding RNAs based on feature relationship and find that the feature relationship between ORF (open reading frame) length and GC content presents universally substantial divergence in lncRNAs and protein-coding RNAs, as observed in a broad variety of species. Based on the feature relationship, accordingly, we further present LGC, a novel algorithm for identifying lncRNAs that is able to accurately distinguish lncRNAs from protein-coding RNAs in a cross-species manner without any prior knowledge. As validated on large-scale empirical datasets, comparative results show that LGC outperforms existing algorithms by achieving higher accuracy, well-balanced sensitivity and specificity, and is robustly effective (>90% accuracy) in discriminating lncRNAs from protein-coding RNAs across diverse species that range from plants to mammals. To our knowledge, this study, for the first time, differentially characterizes lncRNAs and protein-coding RNAs based on feature relationship, which is further applied in computational identification of lncRNAs. Taken together, our study represents a significant advance in characterization and identification of lncRNAs and LGC thus bears broad potential utility for computational analysis of lncRNAs in a wide range of species.

bioinformatics↗

bioRxiv2018

Screening of FDA-approved Drugs and Identification of Novel Lassa Virus Entry Inhibitors

Lassa virus (LASV) belongs to the Mammarenavirus genus (family Arenaviridae) and causes severe hemorrhagic fever in humans. At present, there are no Food and Drug Administration (FDA)-approved drugs or vaccines specific for LASV. Herein, high-throughput screening of an FDA-approved drug library was performed against LASV entry using a pseudo-type virus enveloping LASV glycoproteins. Two hit drugs, lacidipine and phenothrin, were identified as LASV entry inhibitors in the micromolar range. A mechanistic study revealed that both drugs inhibited LASV entry by blocking low-pH-induced membrane fusion. Moreover, lacidipine irreversibly bound to the LASV glycoprotein complex (GPC), resulting in virucidal activity. Adaptive mutant analyses demonstrated that replacement of T40, located in the ectodomain of the stable-signal peptide (SSP), with lysine (K) conferred LASV resistance to lacidipine without apparent loss of the viral growth profile. Furthermore, lacidipine showed antiviral activity and specificity against both LASV and the Guanarito virus (GTOV), which is also a category A new world arenavirus. Drug-resistant variants indicate that the V36M in ectodomain of SSP mutant and V436A in the transmembrane domain of GP2 mutant conferred GTOV resistance to lacidipine, suggesting that lacidipine might act via a novel mechanism other than calcium inhibition. This study shows that both lacidipine and phenothrin are candidates for LASV therapy, and the membrane-proximal external region of the GPC might provide an entry-targeted platform for inhibitors.

microbiology↗

bioRxiv2018

Single-Nucleotide-Resolution Computing and Memory in Living Cells

Computing and memory in living cells are central to encoding next-generation therapies and studying in situ biology, but existing strategies have limited encoding capacity and are challenging to scale. To overcome this bottleneck, we developed a highly scalable, robust and compact platform for encoding logic and memory operations in living bacterial and human cells. This platform, named DOMINO for DNA-based Ordered Memory and Iteration Network Operator, converts DNA in living cells into an addressable, readable, and writable computation and storage medium via a single-nucleotide resolution read-write head that enables dynamic and highly efficient DNA manipulation. We demonstrate that the order and combination of DNA writing events can be programmed by biological cues and multiple molecular recorders can be coordinated to encode a wide range of order-independent, sequential, and temporal logic and memory operations. Furthermore, we show that these operators can be used to perform both digital and analog computation, and record signaling dynamics and cellular states in a long-term, autonomous, and minimally disruptive fashion. Finally, we show that the platform can be functionalized with gene regulatory modules and interfaced with cellular circuits to continuously monitor cellular phenotypes and engineer gene circuits with artificial learning capacities. We envision that highly scalable, compact, and modular DOMINO operators will lay the foundation for building robust and sophisticated synthetic gene circuits for numerous biotechnological and biomedical applications.\n\nOne Sentence SummaryA programmable read-write head with single-nucleotide-resolution for genomic DNA enables robust and scalable computing and memory operations in living cells.

synthetic biology↗

bioRxiv2018

Adaptive and Wireless Recordings of Electrophysiological Signals during Concurrent Magnetic Resonance Imaging

Strong electromagnetic fields that occur during functional magnetic resonance imaging (fMRI) presents a challenging environment for concurrent electrophysiological recordings. Here, we present a miniaturized, wireless platform - \"MR-Link\" (Multimodal Recording Link) that provides a hardware solution for simultaneous electrophysiological and fMRI signal acquisition. The device detects the changes in the electromagnetic field during fMRI to synchronize amplification and sampling of electrophysiological signals with minimal artifacts. It wirelessly transmits the recorded data at a frequency detectable by the MR-receiver coil. The transmitted data is readily separable from MRI in the frequency domain. To demonstrate its efficacy, we used this device to record electrocardiograms and somatosensory evoked potential during concurrent fMRI scans. The device minimized the fMRI-induced artifacts in electrophysiological data and wirelessly transmitted the data back to the receiver coil without compromising fMRI signal quality. The device is compact (22 mm dia., 2gms) and can be placed within the MR-bore to precisely synchronize with fMRI. Therefore, MR-Link offers an inexpensive system by eliminating the need for amplifiers with a high dynamic range, high-speed sampling, additional storage or synchronization hardware for electrophysiological signal acquisition. It is expected to enable a broader range of applications of simultaneous fMRI and electrophysiology in animals and humans.

bioengineering↗

bioRxiv2018

Vagus Nerve Stimulation Promotes Gastric Emptying by Increasing Pyloric Opening Measured with Magnetic Resonance Imaging

BackgroundVagus nerve stimulation (VNS) is an emerging electroceutical therapy for remedying gastric disorders that are poorly managed by pharmacological treatments and/or dietary changes. Such therapy seems promising since the vagovagal neurocircuitry controlling the enteric nervous system strongly influences gastric functions.\n\nMethodsHere, the modulatory effects of left cervical VNS on gastric emptying in rats was quantified using a 1) feeding protocol in which the animal voluntarily consumed a post-fast, gadolinium-labeled meal and 2) newly developed, robust, sensitive and non-invasive imaging strategy to measure antral motility, pyloric activity and gastric emptying based on contrast-enhanced magnetic resonance imaging (MRI) and computer-assisted image processing pipelines.\n\nKey ResultsVNS significantly accelerated gastric emptying (control vs. VNS: 24.9{+/-}3.5% vs. 40.7{+/-}3.9% of meal emptied per 4hrs, p<0.05). This effect resulted from a greater relaxation of the pyloric sphincter (control vs. VNS: 1.4{+/-}0.2 vs. 2.5{+/-}0.5 mm2 cross-sectional area of lumen, p<0.05), without notable changes in antral contraction amplitude (control vs. VNS: 30.6{+/-}3.0% vs. 32.5{+/-}3.0% occlusion), peristaltic velocity (control vs. VNS: 0.67{+/-}0.03 vs. 0.67{+/-}0.03 mm/s), or frequency (control vs. VNS: 6.3{+/-}0.1 vs. 6.4{+/-}0.2 cpm). The degree to which VNS relaxed the pylorus positively correlated with gastric emptying rate (r = 0.5465, p<0.01).\n\nConclusions & InferencesThe MRI protocol employed in this study is expected to enable advanced preclinical studies to understand stomach pathophysiology and its therapeutics. Results from this study suggest an electroceutical treatment approach for gastric emptying disorders using cervical VNS to control the degree of pyloric sphincter relaxation.\n\nKey PointsO_LIVagus nerve stimulation is emerging as a new electroceutical therapy for treating gastric disorders. However, its underlying mechanism(s) and therapeutic effect(s) remain incompletely understood.\nC_LIO_LIVagus nerve stimulation significantly accelerated gastric emptying by promoting the relaxation of the pyloric sphincter.\nC_LIO_LIMRI offers high spatial and temporal resolution to non-invasively characterize gastric motility and physiology in preclinical animal models.\nC_LI

bioengineering↗

bioRxiv2017

STIMULUS: Noninvasive Dynamic Patterns of Neurostimulation using Spatio-Temporal Interference

Using a systematic computational and modeling framework, we provide a novel Spatio-Temporal Interference-based stiMULation focUsing Strategy (STIMULUS) for high spatial precision noninvasive neurostimulation deep inside the brain. To do so, we first replicate the results of the recently proposed temporal interference (TI) stimulation (which was only tested in-vivo) in a computational model based on a Hodgkin-Huxley model for neurons and a model of current dispersion in the head. Using this computational model, we obtain a nontrivial extension of the 2-electrode-pair TI proposed originally to multielectrode TI (> 2 electrode pairs) that yields significantly higher spatial precision. To further improve precision, we develop STIMULUS techniques for generating spatial interference patterns in conjunction with temporal interference, and demonstrate strict and significant improvements over multielectrode TI. Finally, we utilize the adaptivity that is inherent in STIMULUS to create multisite neurostimulation patterns that can be dynamically steered over time.

neuroscience↗

bioRxiv2017

HDAC11 regulates type I interferon signaling through defatty-acylation of SHMT2

The smallest histone deacetylase (HDAC) and the only class IV HDAC member, HDAC11, is reported to regulate immune activation and tumorigenesis, yet its physiological function is largely unknown. Here we identify HDAC11 as an efficient lysine defatty-acylase that is >10,000-fold more efficient than its deacetylase activity. Through proteomics studies, we identified SHMT2 as a defatty-acylation substrate of HDAC11. HDAC11-catalyzed defatty-acylation did not affect the enzymatic activity of SHMT2. Instead, it affects the ability of SHMT2 to regulate type I interferon receptor ubiquitination and internalization. Correspondingly, HDAC11 depletion increased type I interferon signaling in both cell culture and mice. This study is the first time a zinc-dependent HDAC is found to have an activity that is much more efficient than the corresponding deacetylase activity. The finding expands the physiological functions of HDAC11 and protein lysine fatty acylation, and opens up opportunities to develop HDAC11-specific inhibitors as therapeutics to modulate immune responses.

biochemistry↗

bioRxiv2017

Vagal Nerve Stimulation Triggers Wide-Spread Evoked Responses and Changes in Large-Scale Functional Connectivity in Rat Brains

Vagus nerve stimulation (VNS) is a therapy for epilepsy and depression. However, its efficacy varies and its mechanism remains unclear. Prior studies have used functional magnetic resonance imaging (fMRI) to map brain activations with VNS in human brains, but have reported inconsistent findings. The source of inconsistency is likely attributable to the complex temporal characteristics of VNS-evoked fMRI responses that cannot be fully explained by simplified response models in the conventional model-based analysis for activation mapping. To address this issue, we acquired 7-Tesla blood oxygenation level dependent fMRI data from anesthetized Sprague-Dawley rats receiving electrical stimulation at the left cervical vagus nerve. Using spatially independent component analysis, we identified 20 functional brain networks and detected the network-wise activations with VNS in a data-driven manner. Our results showed that VNS activated 15 out of 20 brain networks, and the activated regions covered >76% of the brain volume. The time course of the evoked response was complex and distinct across regions and networks. In addition, VNS altered the strengths and patterns of correlations among brain networks relative to those in the resting state. The most notable changes in network-network interactions were related to the limbic system. Together, such profound and widespread effects of VNS may underlie its unique potential for a wide range of therapeutics to relieve central or peripheral conditions.

neuroscience↗

bioRxiv2017

Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing

Conventional methods for profiling the molecular content of biological samples fail to resolve heterogeneity that is present at the level of single cells. In the past few years, single cell RNA sequencing has emerged as a powerful strategy for overcoming this challenge. However, its adoption has been limited by a paucity of methods that are at once simple to implement and cost effective to scale massively. Here, we describe a combinatorial indexing strategy to profile the transcriptomes of large numbers of single cells or single nuclei without requiring the physical isolation of each cell (Single cell Combinatorial Indexing RNA-seq or sci-RNA-seq). We show that sci-RNA-seq can be used to efficiently profile the transcriptomes of tens-of-thousands of single cells per experiment, and demonstrate that we can stratify cell types from these data. Key advantages of sci-RNA-seq over contemporary alternatives such as droplet-based single cell RNA-seq include sublinear cost scaling, a reliance on widely available reagents and equipment, the ability to concurrently process many samples within a single workflow, compatibility with methanol fixation of cells, cell capture based on DNA content rather than cell size, and the flexibility to profile either cells or nuclei. As a demonstration of sci-RNA-seq, we profile the transcriptomes of 42,035 single cells from C. elegans at the L2 stage, effectively 50-fold \"shotgun cellular coverage\" of the somatic cell composition of this organism at this stage. We identify 27 distinct cell types, including rare cell types such as the two distal tip cells of the developing gonad, estimate consensus expression profiles and define cell-type specific and selective genes. Given that C. elegans is the only organism with a fully mapped cellular lineage, these data represent a rich resource for future methods aimed at defining cell types and states. They will advance our understanding of developmental biology, and constitute a major step towards a comprehensive, single-cell molecular atlas of a whole animal.

genomics↗