Biology subjects

Zhang, C.

Publications and source records attributed to Zhang, C..

At least 901 records · Page 50Linked to original sources

bioRxiv2020

Enhanced meningeal lymphatic drainage ameliorates neuroinflammation and hepatic encephalopathy in cirrhotic rats

Background and aimsHepatic encephalopathy (HE) is a serious neurological complication in patients with liver cirrhosis. Nothing is known about the role of the meningeal lymphatic system in HE. We tested our hypothesis that enhancement of meningeal lymphatic drainage could decrease neuroinflammation and ameliorate HE. MethodsA 4-week bile duct ligation (BDL) model was used to develop cirrhosis with HE in rats. Brain inflammation in patients with HE was evaluated using archived GSE41919. Motor function of rats was assessed by the rotarod test. AAV8-VEGF-C was injected into the cisterna magna of BDL rats one day after surgery to induce meningeal lymphangiogenesis. ResultsCirrhotic rats with HE showed significantly increased microglia activation in the middle region of the cortex (p<0.001) as well as increased neuroinflammation as indicated by significant increases in IL-1{beta}, INF{gamma}, TNF and Iba1 expression in at least one of the three regions of the cortex. Motor function was also impaired in rats with HE (p<0.05). Human brains of cirrhotic patients with HE also exhibited upregulation of pro-inflammatory genes (NF-{kappa}{beta}, Iba1, TNF and IL-1{beta}) (n=6). AAV8-VEGF-C injection significantly increased meningeal lymphangiogenesis (p=0.035) and tracer dye uptake in the anterior and middle regions of the cortex (p=0.006 & 0.003, respectively), their corresponding meninges (p=0.086 & 0.006, respectively) and the draining lymph nodes (p=0.02). Further, AAV8-VEGF-C decreased microglia activation (p<0.001) and neuroinflammation, and ameliorated motor dysfunction (p=0.024). ConclusionPromoting meningeal lymphatic drainage and enhancing waste clearance improves HE. Manipulation of meningeal lymphangiogenesis could be a new therapeutic strategy for the treatment of HE.

neuroscience↗

bioRxiv2020

BLOS1 mediates kinesin switch during endosomal recycling of LDL receptor

Low-density lipoprotein receptor (LDLR) in hepatocytes plays a key role in normal clearance of circulating LDL and in whole body cholesterol homeostasis. The trafficking of LDLR is highly regulated in clathrin-dependent endocytosis, endosomal recycling and lysosomal degradation. Current studies have been focusing on its endocytosis and degradation. However, the detailed molecular and cellular mechanisms underlying its endosomal recycling are largely unknown. We found that BLOS1, a shared subunit of BLOC-1 and BORC, is involved in LDLR endosomal recycling. Loss of BLOS1 leads to less membrane LDLR and impairs LDL clearance from plasma in hepatocyte-specific BLOS1 knockout mice. BLOS1 interacts with kinesin-3, and that BLOS1 acts as a new adaptor for kinesin-2 to coordinate kinesin-3 and kinesin-2 during the long-range transport of recycling endosomes (REs) to plasma membrane along microtubule tracks to overcome hurdles at microtubule intersections. These findings provide new insights into REs anterograde transport and the pathogenesis of dyslipidemia.

cell biology↗

bioRxiv2020

A shared neural substrate for action verbs and observed actions in human posterior parietal cortex.

High-level sensory and motor cortical areas are activated when processing the meaning of language, but it is unknown whether, and how, words share a neural substrate with corresponding sensorimotor representations. We recorded from single neurons in human posterior parietal cortex (PPC) while participants viewed action verbs and corresponding action videos from multiple views. We find that PPC neurons exhibit a common neural substrate for action verbs and observed actions. Further, videos were encoded with mixtures of invariant and idiosyncratic responses across views. Action verbs elicited selective responses from a fraction of these invariant and idiosyncratic neurons, without preference, thus associating with a statistical sampling of the diverse sensory representations related to the corresponding action concept. Controls indicated the results are not the product of visual imagery nor arbitrary learned associations. Our results suggest that language may activate the consolidated visual experience of the reader.

neuroscience↗

bioRxiv2020

Visual function restoration in genetically blind mice via endogenous cellular reprogramming

In this study, we developed an in-situ cellular reprogramming strategy for potent restoration of vision in advanced/end-stage retinitis pigmentosa (RP). Via repressing PTB, an RNA binding protein critical for converting non-neuronal cells to the neuronal lineage, we successfully reprogramed Muller glia to a retinal neuronal fate, and then to cones. We demonstrated that this cellular reprogramming approach was able to rescue retinal photoreceptor degeneration and restore visual functions in two RP mouse models with total blindness, suggesting a novel universal strategy for treating end-stage degenerative diseases.

cell biology↗

bioRxiv2020

Leveraging mRNAs sequences to express SARS-CoV-2 antigens in vivo

SARS-CoV-2 has rapidly become a pandemic worldwide; therefore, an effective vaccine is urgently needed. Recently, messenger RNAs (mRNAs) have emerged as a promising platform for vaccination. Here, we systematically investigated the untranslated regions (UTRs) of mRNAs in order to enhance protein production. Through a comprehensive analysis of endogenous gene expression and de novo design of UTRs, we identified the optimal combination of 5 and 3 UTR, termed as NASAR, which was five to ten-fold more efficient than the tested endogenous UTRs. More importantly, NASAR mRNAs delivered by lipid-derived nanoparticles showed dramatic expression of potential SARS-CoV-2 antigens both in vitro and in vivo. These NASAR mRNAs merit further development as alternative SARS-CoV-2 vaccines.

bioengineering↗

bioRxiv2020

High-affinity agonist binding to C5aR results from a cooperative two-site binding mechanism

A current challenge in the field of life sciences is to decipher, in their native environment, the functional activation of cell surface receptors upon binding of complex ligands. Lack of suitable nanoscopic methods has hampered our ability to meet this challenge in an experimental manner. Here, we use for the first time the interplay between atomic force microscopy, steered molecular dynamics and functional assays to elucidate the complex ligand-binding mechanism of C5a with the human G protein-coupled C5a receptor (C5aR). We have identified two independent binding sites acting in concert where the N-terminal C5aR serves as kinetic trap and the transmembrane domain as functional site. Our results corroborate the two-site binding model and clearly identify a cooperative effect between two binding sites within the C5aR. We anticipate that our methodology could be used for development and design of new therapeutic agents to negatively modulate C5aR activity.

biochemistry↗

bioRxiv2020

Principles of mRNA control by human PUM proteins elucidated from multi-modal experiments and integrative data analysis

The human PUF-family proteins, PUM1 and PUM2, post-transcriptionally regulate gene expression by binding to a PUM recognition element (PRE) in the 3 UTR of target mRNAs. Hundreds of PUM1/2 targets have been identified from changes in steady state RNA levels; however, prior studies could not differentiate between the contributions of changes in transcription and RNA decay rates. We applied metabolic labeling to measure changes in RNA turnover in response to depletion of PUM1/2, showing that human PUM proteins regulate expression almost exclusively by changing RNA stability. We also applied an in vitro selection workflow to precisely identify the binding preferences of PUM1 and PUM2. By integrating our results with prior knowledge, we developed a rulebook of key contextual features that differentiate functional vs. non-functional PREs, allowing us to train machine learning models that accurately predict the functional regulation of RNA targets by the human PUM proteins.

molecular biology↗

bioRxiv2020

Differential responses of transplanted stem cells to the diseased environment unveiled by a single molecular NIR II cell tracker

Stem cell therapy holds high promises in regenerative medicine. The major challenge of clinical translation is to precisely and quantitatively evaluate the in vivo cell distribution, migration, and engraftment, which cannot be easily achieved by current techniques. To address this issue, for the first time, we have developed a single molecular cell tracker with a strong fluorescence signal in the second near-infrared (NIR-II) window (1000-1700 nm) for real-time monitoring of in vivo cell behaviors in both healthy and diseased animal models. The NIR-II tracker (CelTrac1000) has shown complete cell labeling with low cytotoxicity and profound long-term tracking ability for 30 days in high temporospatial resolution for semi-quantification of the biodistribution of primary mesenchymal stem cell and induced pluripotent stem cell-derived endothelial cells. Taking advantage of the unique merits of CelTrac1000, the responses of transplanted stem cells to different diseased environments have been discriminated and unveiled. Furthermore, we also demonstrate CelTrac1000 as a universal and effective technique for ultrafast real-time tracking of the cellular migration and distribution in a single cell cluster resolution, along with the lung contraction and heart beating. As such, this single molecular NIR-II tracker will shift the optical cell tracking into a single cell cluster and millisecond temporospatial resolution for better evaluating and understanding stem cell therapy, affording optimal doses and efficacy. Significance StatementFor the first time, we synthesized a NIR-II tracker (CelTrac1000) for ultrafast real-time tracking of the migration trajectory of transplanted mesenchymal stem cells in the circulatory system with a single cell cluster resolution. Taking advantage of the merits of CelTrac1000, the responses of transplanted stem cells to different diseased environments, including acute lung injury, myocardial infarction, and middle cerebral artery occlusion, have been discriminated and unveiled in mice models. As such, our approach can help correlate critical biomedical information in stem cell therapies, such as stem cell dosing and engraftment and their relationships with efficacy, providing more accurate therapeutic treatment and outcomes in certain diseases during a long evaluation period (>30 days) in comparison with the commercial Qtracker (7-10 days).

bioengineering↗

bioRxiv2020

Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites

The outbreak of coronavirus disease (COVID-19) in China caused by SARS-CoV-2 virus continually lead to worldwide human infections and deaths. It is currently no specific viral protein targeted therapeutics yet. Viral nucleocapsid protein is a potential antiviral drug target, serving multiple critical functions during the viral life cycle. However, the structural information of SARS-CoV-2 nucleocapsid protein is yet to be clear. Herein, we have determined the 2.7 [A] crystal structure of the N-terminal RNA binding domain of SARS-CoV-2 nucleocapsid protein. Although overall structure is similar with other reported coronavirus nucleocapsid protein N-terminal domain, the surface electrostatic potential characteristics between them are distinct. Further comparison with mild virus type HCoV-OC43 equivalent domain demonstrates a unique potential RNA binding pocket alongside the {beta}-sheet core. Complemented by in vitro binding studies, our data provide several atomic resolution features of SARS-CoV-2 nucleocapsid protein N-terminal domain, guiding the design of novel antiviral agents specific targeting to SARS-CoV-2.

molecular biology↗

bioRxiv2020

TWIRLS, an automated topic-wise inference method based on massive literature, suggests a possible mechanism via ACE2 for the pathological changes in the human host after coronavirus infection

Faced with the current large-scale public health emergency, collecting, sorting, and analyzing biomedical information related to the "coronavirus" should be done as quickly as possible to gain a global perspective, which is a basic requirement for strengthening epidemic control capacity. However, for human researchers studying the viruses and the hosts, the vast amount of information available cannot be processed effectively and in a timely manner, particularly when the scientific understanding may be limited, which can further lower the information processing efficiency. We present TWIRLS, a method that can automatically acquire, organize, and classify information. Additionally, independent functional data sources can be added to build an inference system using a machine-based approach, which can provide relevant knowledge to help human researchers quickly establish subject cognition and to make more effective decisions. TWIRLS can automatically analyze more than three million words in more than 14,000 literature articles in only 4 hours. Combining with generalized gene interaction databases creates a data interface that can help researchers to further analyze the information. Using the TWIRLS system, we found that an important regulatory factor angiotensin-converting enzyme 2 (ACE2) may be involved in the host pathological changes on binding to the coronavirus after infection. After triggering functional changes in ACE2/AT2R, an imbalance in the steady-state cytokine regulatory axis involving the Renin-Angiotensin System and IP-10 leads to a cytokine storm.

bioinformatics↗

bioRxiv2020

Endosidin20 is a broad-spectrum cellulose synthesis inhibitor with an herbicidal function

Cellulose is an important component of plant cell wall that controls anisotropic cell growth. Disruption of cellulose biosynthesis often leads to inhibited cell growth. Endosidin20 (ES20) was recently identified as a cellulose biosynthesis inhibitor (CBI) that targets the catalytic domain of Arabidopsis cellulose synthase 6 (CESA6) to inhibit plant growth. Here, we characterized the effects of ES20 on the growth of some other plant species and found that ES20 is a broad-spectrum plant growth inhibitor. We compared the inhibitory effects of ES20 and other CBIs on the growth of cesa6 plants that have reduced sensitivity to ES20. We found that most of the cesa6 with reduced sensitivity to ES20 show normal inhibited growth by other CBIs. ES20 also shows synergistic inhibitory effect on plant growth when applied together with other CBIs. We show ES20 has a different mode of action than tested CBIs isoxaben, indaziflam and C17. ES20 not only inhibits Arabidopsis growth under tissue culture condition, it inhibits plant growth under soil condition after direct spraying. We demonstrate that plants carrying two missense mutations can tolerate dual inhibition by ES20 and isoxaben. One sentence summaryCellulose biosynthesis inhibitor Endosidin20 has synergistic effect with other cellulose synthesis inhibitors and has the potential to be used as a spray herbicide.

plant biology↗

bioRxiv2020

C. elegans nuclear RNAi factor SET-32 deposits the transgenerational heritable histone modification, H3K23me3

Nuclear RNAi provides a highly tractable system to study RNA-mediated chromatin changes and epigenetic inheritance. Recent studies have indicated that the regulation and function of nuclear RNAi-mediated heterochromatin are highly complex. Our knowledge of histone modifications and the corresponding histone modifying enzymes involved in the system remains limited. In this study, we show that the heterochromatin mark, H3K23me3, is induced by nuclear RNAi at both exogenous and endogenous targets in C. elegans. In addition, dsRNA-induced H3K23me3 can be inherited for four generations. We demonstrate that the histone methyltransferase SET-32, methylates H3K23 in vitro. Both set-32 and the germline nuclear RNAi Argonaute, hrde-1, are required for nuclear RNAi-induced H3K23me3 in vivo. Our data poise H3K23me3 as an additional chromatin modification in the nuclear RNAi pathway and provides the field with a new target for uncovering the role of heterochromatin in transgenerational epigenetic silencing.

molecular biology↗

bioRxiv2020

Sphingolipids with Very Long-chain Fatty Acids Regulate Vacuole Fusion During Tethering and Docking

Sphingolipids are essential in membrane trafficking and cellular homeostasis. Here, we show that sphingolipids containing very long-chain fatty acids (VLCFAs) promote robust homotypic vacuolar fusion in Saccharomyces cerevisiae. The elongase Elo3 adds two carbons to 24-carbon (C24) acyl chains to make C26 VLCFAs that are incorporated into sphingolipids. Vacuoles isolated from elo3{Delta} cells had increased fluidity relative to the wild-type and were attenuated for fusion. Upon further testing we found that vesicle the tethering stage was affected as elo3{Delta} vacuole clusters contained fewer vesicles versus the WT. Vacuole tethering requires the interactions of late endosomal Rab GTPase Ypt7 and the HOPS tethering complex. Pulldown assays using GST-Ypt7 showed that HOPS from elo3{Delta} vacuole extracts failed to bind Ypt7 while HOPS from WT extracts interacted with GST-Ypt7. Furthermore GFP-Ypt7 failed to localize at vertex microdomains of elo3{Delta} vacuoles relative to the WT, whereas HOPS and regulatory lipids did accumulate at vertices. Finally, we found that elo3{Delta} vacuoles had reduced V-ATPase. Together these data show that C26-VLCFA containing sphingolipids are important for Ytp7 function and vacuole homeostasis.

cell biology↗

bioRxiv2020

Endosidin20 targets cellulose synthase catalytic domain to inhibit cellulose biosynthesis

Cellulose is synthesized by rosette structured cellulose synthase (CESA) complexes (CSCs), each of which is composed of multiple units of CESAs in three different isoforms. CSCs rely on vesicle trafficking for delivery to the plasma membrane where they catalyze cellulose synthesis. Although the rosette structured CSCs were observed decades ago, it remains unclear what amino acids in plant CESA that directly participate in cellulose catalytic synthesis. It is also not clear how the catalytic activity of CSCs influences their efficient transport at the subcellular level. Here we report characterization of the small molecule Endosidin20 (ES20) and present evidence that it represents a new CESA inhibitor. We show data from chemical genetic analyses, biochemical assays, structural modeling, and molecular docking to support our conclusion that ES20 targets the catalytic site of Arabidopsis CESA6. Further, chemical genetic analysis reveals important amino acids that potentially form the catalytic site of plant CESA6. Using high spatiotemporal resolution live-cell imaging, we found that inhibition of CSC catalytic activity by inhibitor treatment, or by creating missense mutation at amino acids in the predicted catalytic site, causes reduced efficiency in CSC transport to the plasma membrane. Our results show that the catalytic activity of plant CSCs is integrated with subcellular trafficking dynamics. One sentence summaryEndosidin20 targets cellulose synthase at the catalytic site to inhibit cellulose synthesis and the inhibition of catalytic activity reduces cellulose synthase complex delivery to the plasma membrane.

plant biology↗

bioRxiv2020

Antagonistic roles of NOT1 paralogues in the timing of gene expression in Plasmodium falciparum

NOT1 is the scaffold of the CCR4-NOT complex, a highly conserved multi-protein complex that regulates gene expression in eukaryotes. As opposed to most eukaryotes in which NO1 is encoded by a single gene, malaria parasites, Plasmodium falciparum, carry two NOT1 paralogues, PfNOT1.1 and PfNOT1.2. Here we showed that the two PfNOT1 proteins function as mutually exclusive scaffolds within the PfCCR4-NOT protein complexes that are abundantly located in the parasite cytoplasm. Intriguingly, the two PfNOT1 paralogues appear to have directly opposing functions in regulation of mRNA abundance across the P. falciparum IDC, in which PfNTO1.1 and PfNOT1.2 induces and suppresses transcript abundance during their active transcription, respectively. Targeted disruption of either of the PfNOT1 gene causes defective growth and lower invasion rates presumably due to the deregulation the P. falciparum IDC transcriptional cascade. We also demonstrate that the regulatory function of both PfNOT1.1 and PfNOT1.2 are related to another PfCCR4-NOT subunit, PfCaf1, which indicates their activity during post-transcriptional regulation. Indeed RNA decay studies suggest the active role of both PfNOT1 proteins in regulation of mRNA stability in a directly opposing manner. Author summaryCCR4-NOT complex is a highly conserved multi-protein complex that regulates gene expression in eukaryotes. NOT1 serves as the scaffold of the complex and plays important roles in gene regulation both transcriptionally and post-transcriptionally. As opposed to other eukaryotes, P. falciparum encodes two paralogues of PfNOT1, raising the question as to the significance to possess an additional copy of PfNOT1 in the parasite. Here we described antagonistic regulatory functions of two PfNOT1 paralogues in gene expression during the 48-hour intraerythrocytic developmental cycle. We also reported that their regulatory functions are predominantly post-transcriptional and proposed a model in which distinct PfCCR4-NOT complexes defined by mutually exclusive PfNOT1 scaffolds differentially regulate PfCAF1 function in mRNA decay. This study highlights the importance of post-transcriptional regulation in P. falciparum and provides novel insights into mechanisms of gene regulation in this organism. The unique presence of two PfNOT1 paralogues may also open avenues for the development of new drug targets for anti-malarial control.

molecular biology↗

bioRxiv2020

Low bias DNA for sustainable and efficient data storage

In DNA data storage, the massive sequence complexity creates challenges in repeatable and efficient information readout. Here, our study clearly demonstrated that canonical polymerase chain reaction (PCR) created significant DNA amplification biases, which greatly hinder fast and stable data retrieving from hundred-thousand synthetic DNA sequences encoding over 2.85 megabyte (MB) digital data. To mitigate the amplification bias, we adapted an isothermal DNA amplification for low-bias amplification of DNA pool with massive sequence complexity, and named the new method isothermal DNA reading (iDR). By using iDR, we were able to robustly and repeatedly retrieve the data stored in DNA strands attached on magnetic beads (MB) with significantly decreased sequencing reads, compared with the PCR method. Therefore, we believe that the low-bias iDR method provides an ideal platform for robust DNA data storage, and fast and reliable data readout.

synthetic biology↗

bioRxiv2020

Protein structure and sequence re-analysis of 2019-nCoV genome does not indicate snakes as its intermediate host or the unique similarity between its spike protein insertions and HIV-1

As the infection of 2019-nCoV coronavirus is quickly developing into a global pneumonia epidemic, careful analysis of its transmission and cellular mechanisms is sorely needed. In this report, we re-analyzed the computational approaches and findings presented in two recent manuscripts by Ji et al. (https://doi.org/10.1002/jmv.25682) and by Pradhan et al. (https://doi.org/10.1101/2020.01.30.927871), which concluded that snakes are the intermediate hosts of 2019-nCoV and that the 2019-nCoV spike protein insertions shared a unique similarity to HIV-1. Results from our re-implementation of the analyses, built on larger-scale datasets using state-of-the-art bioinformatics methods and databases, do not support the conclusions proposed by these manuscripts. Based on our analyses and existing data of coronaviruses, we concluded that the intermediate hosts of 2019-nCoV are more likely to be mammals and birds than snakes, and that the "novel insertions" observed in the spike protein are naturally evolved from bat coronaviruses.

bioinformatics↗

bioRxiv2020

Dual blockade of IL-6 and CTLA-4 regresses pancreatic tumors in a CD4+ T cell-dependent manner.

Pancreatic ductal adenocarcinoma (PDAC) is exceptionally resistant to immune checkpoint inhibition (ICI). We previously reported that elevated systemic interleukin-6 (IL-6) and increased numbers of T cells positive for circulating cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) correlate with worse overall survival in patients with PDAC. We postulated that combined blockade of IL-6 and CTLA-4 would significantly enhance anti-tumor immune responses to PDAC. Dual blockade of IL-6 and CTLA-4 in immune competent mice bearing subcutaneously injected pancreatic tumors significantly inhibited tumor growth, accompanied by overwhelming T cell infiltration. Therapeutic efficacy was confirmed in an orthotopic murine model of pancreatic cancer and T cell depletion studies unveiled a unique dependence on CD4+ T cells for anti-tumor activity of dual IL-6 and CTLA-4 blockade. In vitro studies utilizing T cells from a TRP-1 transgenic mouse as an antigen-specific model system demonstrate this combination therapy elicits increased IFN-{gamma} production by activated CD4+ T cells. Additionally, IFN-{gamma} stimulation of pancreatic tumor cells in vitro profoundly increased tumor cell production of CXCR3 specific chemokines (CXCL10 and CXCL9). Further studies blocking CXCR3 in the presence of combined IL-6 and CTLA-4 blockade prevented orthotopic tumor regression, demonstrating a dependence on the CXCR3 axis for anti-tumor efficacy. We also found combination therapy increased intratumoral CD4+ T cells and elicited systemic changes in T-helper subsets. These data represent the first report of IL-6 and CTLA-4 blockade as a means to regress pancreatic tumors with defined operative mechanisms of efficacy. Given these results, this therapeutic combination has potential for immediate clinical translation. One Sentence SummaryBlockade of interleukin-6 in pancreatic cancer enhances CTLA-4 immune checkpoint inhibition to regress tumors in a CD4+ T cell and CXCR3-dependent manner.

cancer biology↗