Biology subjects

Fan, Z.

Publications and source records attributed to Fan, Z..

103 records · Page 6Linked to original sources

bioRxiv2020

Structural and biochemical characterization of nsp12-nsp7-nsp8 core polymerase complex from COVID-19 virus

The ongoing global pandemic of coronavirus disease 2019 (COVID-19) has caused huge number of human deaths. Currently, there are no specific drugs or vaccines available for this virus. The viral polymerase is a promising antiviral target. However, the structure of COVID-19 virus polymerase is yet unknown. Here, we describe the near-atomic resolution structure of its core polymerase complex, consisting of nsp12 catalytic subunit and nsp7-nsp8 cofactors. This structure highly resembles the counterpart of SARS-CoV with conserved motifs for all viral RNA-dependent RNA polymerases, and suggests the mechanism for activation by cofactors. Biochemical studies revealed reduced activity of the core polymerase complex and lower thermostability of individual subunits of COVID-19 virus as compared to that of SARS-CoV. These findings provide important insights into RNA synthesis by coronavirus polymerase and indicate a well adaptation of COVID-19 virus towards humans with relatively lower body temperatures than the natural bat hosts.

microbiology↗

bioRxiv2020

Single-cell RNA-seq Imputation using Generative Adversarial Networks

Single-cell RNA-sequencing (scRNA-seq) enables the characterization of transcriptomic profiles at the single-cell resolution with increasingly high throughput. However, it suffers from many sources of technical noises, including insufficient mRNA molecules that lead to excess false zero values, termed dropouts. Computational approaches have been proposed to recover the biologically meaningful expression by borrowing information from similar cells in the observed dataset. However, these methods suffer from oversmoothing and removal of natural cell-to-cell stochasticity in gene expression. Here, we propose the generative adversarial networks (GANs) for scRNA-seq imputation (scIGANs), which uses generated cells rather than observed cells to avoid these limitations and balances the performance between major and rare cell populations. Evaluations based on a variety of simulated and real scRNA-seq datasets show that scIGANs is effective for dropout imputation and enhances various downstream analysis. ScIGANs is robust to small datasets that have very few genes with low expression and/or cell-to-cell variance. ScIGANs works equally well on datasets from different scRNA-seq protocols and is scalable to datasets with over 100,000 cells. We demonstrated in many ways with compelling evidence that scIGANs is not only an application of GANs in omics data but also represents a competing imputation method for the scRNA-seq data.

bioinformatics↗

bioRxiv2019

An integrated genomic approach to dissect the genetic landscape regulating the cell-to-cell transfer of a-synuclein

Neuropathological and experimental evidence suggests that the cell-to-cell transfer of a-synuclein has an important role in the pathogenesis of Parkinsons disease (PD). However, the mechanism underlying this phenomenon is not fully understood. We undertook an siRNA, genome-wide high throughput screen to identify genes regulating the cell-to-cell transfer of a-synuclein. We transiently transfected HEK cells stably overexpressing a-synuclein with a construct encoding GFP-2a-aSynuclein-RFP. The cells expressing a-synuclein-RFP through transfection were double positive for GFP and RFP fluorescence, whereas the cells receiving it through transfer were positive only for RFP fluorescence. The amount of a-synuclein transfer was quantified by high content microscopy. A series of unbiased screens confirmed the involvement of 38 genes in the regulation of a-synuclein-RFP transfer. One of those hits was ITGA8, a candidate gene recently identified through a large PD genome wide association study (GWAS). Weighted gene co-expression network analysis (WGCNA) and weighted protein-protein network interaction analysis (WPPNIA) showed that the hits clustered in networks that included known PD Mendelian and GWAS risk genes more frequently than expected than random chance. Given the genetic overlap between a-synuclein transfer and PD, those findings provide supporting evidence for the importance of the cell-to-cell transfer of a-synuclein in the pathogenesis of PD, and expand our understanding of the mechanism of a-synuclein spread.

neuroscience↗

bioRxiv2019

Out of the Qinghai-Tibetan Plateau and get flourishing - the evolution of Neodon voles (Rodentia: Cricetidae) revealed by systematic sampling and low coverage whole genome sequencing

Neodon, genus of a short time evolutionary history, was reported to be diverged from its relatives in early stage of Pleistocene. Only 4 species were well documented in Neodon for a long period of time until last years when a systematic work described and added three new species, adjusted three species used to belong to Lasiopodomys, Phaiomys, Microtus to Neodon and removed one species (Neodon juldaschi) to genus Blanfordimys, leading to a total of eight species recorded in Neodon. To gain a better insight into the phylogeny and ecology of Neodon, we have systematically sampled Neodon species along the whole Hengduan and Himalayan Mountains in the last 20 years. In addition to morphological identification, we generated 1x - 15x whole genome sequencing (WGS) data and achieved the mitochondrial genomes and an average of 5,382 nuclear genes for each morpho-species. Both morphology and phylogeny results supported an extra six new species in Neodon (nominated Neodon shergylaensis sp. nov., N. namchabarwaensis sp. nov., N. liaoruii sp. nov., N. chayuensis sp. nov., N. bomiensis sp. nov., and N. bershulaensis sp. nov.). This is the first study that included Neodon samples covering its entire distribution area in China and this systematic sampling also revealed a long-time underestimation of Neodons diversity, and suggested its speciation events linked highly to founder event via dispersal (from Plateau to surrounding mountains). The results also revealed that the Qinghai-Tibetan Plateau is the center of origin of Neodon, and the impetus of speciation include climate change, isolation of rivers and mountains.

zoology↗

bioRxiv2019

Reproducible observations revealing patterns of the default mode network underlie rumination

Rumination is a repetitive self-referential thinking style and posited to be an expression of abnormalities in the default mode network (DMN) in major depressive disorder (MDD). Recent evidences indicate DMN is not a unitary network but can be further divided into 3 functionally heterogenous subsystems. However, the subsystem mechanism through which DMN underlie rumination remain unclear. Here, with a modified continuous state-like paradigm, we induced healthy participants to ruminate or imagine objective scenarios (as a distraction control condition) on 3 different MRI scanners. We compared functional connectivities (FC) and inter-subject correlations (ISC) of the DMN and its 3 subsystems between rumination and distraction states. Results yielded a highly reproducible and dissociated pattern. During rumination, within-DMN FC was generally decreased compared to the distraction state. At the subsystem level, we found increased FC between the core and medial temporal lobe (MTL) subsystem and decreased FC between the core and dorsal medial prefrontal cortex (DMPFC) subsystem and within the MTL subsystem. Furthermore, we found decreased ISC within the MTL subsystem. These results suggest a specific and less synchronous activity pattern of DMN during rumination and shed new light on the association between rumination and DMN substrates regarding MDD.

neuroscience↗

bioRxiv2019

A unity of opposites in between Nrf1- and Nrf2-mediated responses to the endoplasmic reticulum stressor tunicamycin

The water-soluble Nrf2 is accepted as a master regulator of antioxidant responses to cellular stress, it was also identified as a direct target of the endoplasmic reticulum (ER)-anchored PERK. However, the membrane-bound Nrf1 response to ER stress remains elusive. Herein, we report a unity of opposites in both Nrf1- and Nrf2-coordinated responses to the ER stressor tunicamycin (TU). The TU-inducible transcription of Nrf1 and Nrf2, as well as GCLM and HO-1, was accompanied by activation of ER stress signaling networks. The unfolded protein response (UPR) mediated by ATF6, IRE1 and PERK was significantly suppressed by Nrf1-specific knockout, but hyper-expression of Nrf2, GCLM and HO-1 was retained in Nrf1-/- cells. By contrast, Nrf2-/-{Delta}TA cells with a genomic deletion of its transactivation domain resulted in significant decreases of GCLM, HO-1 and Nrf1; this was accompanied by partial decreases of IRE1 and ATF6, but not PERK, along with an obvious increase of ATF4. Notably, Nrf1 glycosylation and its trans-activity to mediate transcriptional expression of 26S proteasomal subunits were repressed by TU. This inhibitory effect was enhanced by Nrf1-/- and Nrf2-/-{Delta}TA, but not by a constitutive activator caNrf2{Delta}N (that increased abundances of non-glycosylated and processed Nrf1). Furthermore, caNrf2{Delta}N also enhanced induction of PERK and IRE1 by TU, but reduced expression of ATF4 and HO-1. Such distinct roles of Nrf1 and Nrf2 are unified to maintain cell homeostasis by a series of coordinated ER-to-nuclear signaling responses to TU. Overall, Nrf1 acts in a cell-autonomous manner to determine transcription of most of UPR-target genes, albeit Nrf2 is also partially involved in this process.

molecular biology↗

bioRxiv2019

Bone marrow transplantation rescues monocyte recruitment defect and improves cystic fibrosis in mice

One Sentence SummaryIn this study, we demonstrate that correcting the monocyte adhesion defect in CFTR{Delta}F508 mice (CF mice) by bone marrow transplantation significantly improved survival and reduced inflammation.\n\nAbstractCystic fibrosis (CF) is an inherited life-threatening disease accompanied by repeated lung infections and multi-organ inflammation that affects tens of thousands of people worldwide. The causative gene, cystic fibrosis transmembrane conductance regulator (CFTR), is mutated in CF patients. Monocytes from CF patients show a deficiency in integrin activation and adhesion. Since monocytes play critical roles in controlling infections, defective monocyte function may contribute to CF progression. In this study, we demonstrate that monocytes from CFTR{Delta}F508 mice (CF mice) show defective adhesion under flow. Transplanting CF mice with wild-type bone marrow after sublethal irradiation replaced most (60-80%) CF monocytes with wild-type monocytes, significantly improved survival, and reduced inflammation. Wild-type/CF mixed bone marrow chimeras directly demonstrated defective CF monocyte recruitment to the bronchoalveolar lavage and the intestinal lamina propria in vivo. Our findings show that providing wild-type monocytes by bone marrow transfer rescues gastrointestinal (GI) mortality in CF mice, suggesting that wild-type bone marrow stem cells might mitigate CF inflammation.

immunology↗

bioRxiv2019

Effects of topical PaiTeLing in nude mice implanted with human condyloma acuminatum tissue infected with HPV 6, 31, and 81: comparison with imiquimod and interferon-α-2b

BACKGROUNDThe standard treatment for condyloma acuminatum is topical imiquimod. In the current study, we used a mouse model to compare the effects of an herbal medication PaiTeLing. METHODSLesion tissue was obtained from a woman with genital condyloma acuminatum. DNA genotyping revealed HPV6, 31, and 81. Tissue prism (0.5 cm3) was implanted to BALB/C nude mice, 22 days after the implantation, mice began to receive topical treatment with imiquimod, interferon--2b gel, or PaiTeLing over the site of implantation for 2 consecutive weeks. Mice receiving tissue implantation but no other intervention was included as a control. Skin tissue was collected for H&E staining and anti-CD207 immunohistochemistry. Blood was collected to determine a panel of cytokines. RESULTSH&E staining showed lower number of koilocytes and higher number of Langerhans cells in the treatment groups, particularly in mice receiving imiquimod or PaiTeLing. Blood levels of TNF, IL-2, INF-{gamma} and IL-12p70 were increased in the treatment groups, particularly in mice receiving imiquimod or PaiTeLing. CONCLUSIONImmune response in nude mice infected with HPV6, 31, and 81 is enhanced by treatment with imiquimod, interferon--2b and PaiTeLing. Effects of imiquimod and PaiTeLing seems to be stronger than interferon--2b.

immunology↗

bioRxiv2018

Organized spatial patterns of activated β2 integrins in arresting neutrophils

The transition from leukocyte rolling to firm adhesion is called arrest. {beta}2 integrins are required for neutrophil arrest1. Chemokines can trigger neutrophil arrest in vivo2 and in vitro3. Resting integrins4 exist in a \"bent-closed\" conformation, i.e., not extended (E-) and not high affinity (H-), unable to bind ligand. Electron microscopic images of isolated {beta}2 integrins in \"open\" and \"closed\" conformations5 inspired the switchblade model of integrin activation from E-H- to E+H- to E+H+67. Recently8, we discovered an alternative pathway of integrin activation from E-H- to E-H+ to E+H+. Spatial patterning of activated integrins is thought to be required for effective arrest, but so far only diffraction-limited localization maps of activated integrins exist8. Here, we combine superresolution microscopy with molecular modeling to identify the molecular patterns of H+E-, H-E+, and H+E+ activated integrins on primary human neutrophils. At the time of neutrophil arrest, E+H+ integrins form oriented (non-random) nanoclusters that contain a total of 4,625{+/-}369 E+H+ {beta}2 integrin molecules.

immunology↗

bioRxiv2018

Topovectorial mechanisms control the juxtamembrane proteolytic processing of Nrf1 to remove its N-terminal polypeptides during maturation of the CNC-bZIP factor

The topobiological behaviour of Nrf1 dictates its post-translational modification and its ability to transactivate target genes. Here, we have elucidated that topovectorial mechanisms control the juxtamembrane processing of Nrf1 on the cyto/nucleoplasmic side of endoplasmic reticulum (ER), whereupon it is cleaved and degraded to remove various lengths of its N-terminal domain (NTD, also refold into a UBL module) and acidic domain-1 (AD1) to yield multiple isoforms. Notably, an N-terminal [~]12.5-kDa polypeptide of Nrf1 arises from selective cleavage at an NHB2-adjoining region within NTD, whilst other longer UBL-containing isoforms may arise from proteolytic processing of the protein within AD1 around PEST1 and Neh2L degrons. The susceptibility of Nrf1 to proteolysis is determined by dynamic repositioning of potential UBL-adjacent degrons and cleavage sites from the ER lumen through p97-driven retrotranslocation and -independent pathways into the cyto/nucleoplasm. These repositioned degrons and cleavage sites within NTD and AD1 of Nrf1 are coming into their bona fide functionality, thereby enabling it to be selectively processed by cytosolic DDI-1/2 proteases and also degraded via 26S proteasomes. The resultant proteolytic processing of Nrf1 gives rise to a mature [~]85-kDa CNC-bZIP transcription factor, which regulates transcriptional expression of cognate target genes. Furthermore, putative ubiquitination of Nrf1 is not a prerequisite necessary for involvement of p97 in the client processing. Overall, the regulated juxtamembrane proteolysis (RJP) of Nrf1, though occurring in close proximity to the ER, is distinctive from the mechanism that regulates the intramembrane proteolytic (RIP) processing of ATF6 and SREBP1.

biochemistry↗

bioRxiv2018

Physiological Significance of R-fMRI Indices in Detecting Structural Brain Lesions

Resting-state functional MRI (R-fMRI) research has recently entered the era of \"big data\", however, few studies have provided a rigorous validation of the physiological underpinnings of R-fMRI indices. Although studies have reported that various neuropsychiatric disorders exhibit abnormalities in R-fMRI measures, these \"biomarkers\" have not been validated in differentiating structural lesions (brain tumors) as a concept proof. We enrolled 60 patients with intracranial tumors located in the unilateral cranial cavity and 60 matched normal controls to test whether R-fMRI indices can differentiate tumors, which represents a prerequisite for adapting such indices as biomarkers for neuropsychiatric disorders. Common R-fMRI indices of tumors and their counterpart control regions, which were defined as the contralateral normal areas (for amplitude of low frequency fluctuations (ALFF), fractional ALFF (fALFF), regional homogeneity (ReHo) and degree centrality (DC)) and ipsilateral regions surrounding the tumors (for voxel-mirrored homotopic connectivity (VMHC)), were comprehensively assessed. According to paired t-tests with a Bonferroni correction, only ALFF (both with and without Z-standardization) and VMHC (Fishers r-to-z transformed) could successfully differentiate substantial tumors from their counterpart normal regions in patients. And DC was not able to differentiate tumor from normal unless employed Z-standardization. To validate the lower power in the between-subject design than in the within-subject design, each metric was calculated in a matched control group, and two-sample t-tests were used to compare the patient tumors and the normal controls at the same area. Only ALFF (and that with Z-standardization) along with VMHC succeeded in differentiating significant differences between tumors and the sham tumors areas of normal controls. This study tested the premise of R-fMRI biomarkers for differentiating lesions, and brings a new understanding to physical significance of the Z-standardization.

neuroscience↗

bioRxiv2017

Targeting xCT-Mediated Glutamate Release Normalizes Tumor Angiogenesis In The Brain

Brain tumors are among the most malignant primary tumors, hallmarked by angiogenesis, neuronal destruction and brain swelling. Inhibition of the glutamate-cystein antiporter xCT (system xc-/SLC7A11) alleviates seizures, neuronal cell death and tumor-associated brain edema. Here we show enhanced tumor vessel growth and increased brain edema in xCT-expressing brain tumors. Furthermore, xCT-mediated glutamate impacts directly on endothelial cells in an N-methyl-D-aspartate receptor (NMDAR) dependent manner with intracellular Ca2+ release. Cerebral intravital microscopy revealed that xCT-driven tumor vessels are functional and display increased permeability. Endothelial-cell-specific NMDAR1 knockout mice (GRINi{Delta}EC) show suppressed endothelial sprouting and vascular density compared to control littermates. In addition, implanted gliomas in GRINi{Delta}EC mice display reduced tumor vessels in contrast to gliomas in wildtype animals. Moreover, therapeutic targeting of xCT in gliomas alleviates tumor angiogenesis to normalized levels comparable to controls. Our data reveal that xCT and its substrate glutamate specifically operate on endothelial cells and promote neoangiogenesis. Thus, targeting xCT expression and glutamate secretion in gliomas provides a novel therapeutic roadmap for normalizing tumor angiogenesis.

cell biology↗

bioRxiv2016

Exploring the mutational robustness of nucleic acidsby searching genotype neighbourhoods in sequencespace

To assess the mutational robustness of nucleic acids, many genome- and protein-level studies have been performed; in these investigations, nucleic acids are treated as genetic information carriers and transferrers. However, the molecular mechanism through which mutations alter the structural, dynamic and functional properties of nucleic acids is poorly understood. Here, we performed SELEX in silico study to investigate the fitness distribution of the nucleic acid genotype neighborhood in a sequence space for L-Arm binding aptamer. Although most mutants of the L-Arm-binding aptamer failed to retain their ligand-binding ability, two novel functional genotype neighborhoods were isolated by SELEX in silico and experimentally verified to have similar binding affinity (Kd = 69.3 M and 110.7 M) as the wild-type aptamer (Kd = 114.4 M). Based on data from the current study and previous research, mutational robustness is strongly influenced by the local base environment and ligand-binding mode, whereas bases distant from the binding pocket provide potential evolutionary pathways to approach global fitness maximum. Our work provides an example of successful application of SELEX in silico to optimize an aptamer and demonstrates the strong sensitivity of mutational robustness to the site of genetic variation.

evolutionary biology↗