Biology subjects

Qu, Y.

Publications and source records attributed to Qu, Y..

At least 127 records · Page 7Linked to original sources

bioRxiv2021

Antibody Cocktail Exhibits Broad Neutralization against SARS-CoV-2 and SARS-CoV-2 variants

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has precipitated multiple variants resistant to therapeutic antibodies. In this study, 12 high-affinity antibodies were generated from convalescent donors in early outbreaks using immune antibody phage display libraries. Of them, two RBD-binding antibodies (F61 and H121) showed high affinity neutralization against SARS-CoV-2, whereas three S2-target antibodies failed to neutralize SARS-CoV-2. Following structure analysis, F61 identified a linear epitope located in residues G446 -S494, which overlapped with angiotensin-converting enzyme 2 (ACE2) binding sites, while H121 recognized a conformational epitope located on the side face of RBD, outside from ACE2 binding domain. Hence the cocktail of the two antibodies achieved better performance of neutralization to SARS-CoV-2. Importantly, F61 and H121 exhibited efficient neutralizing activity against variants B.1.1.7 and B.1.351, those showed immune escape. Efficient neutralization of F61 and H121 against multiple mutations within RBD revealed a broad neutralizing activity against SARS-CoV-2 variants, which mitigated the risk of viral escape. Our findings defined the basis of therapeutic cocktails of F61 and H121 with broad neutralization and delivered a guideline for the current and future vaccine design, therapeutic antibody development, and antigen diagnosis of SARS-CoV-2 and its novel variants.

immunology↗

bioRxiv2021

Caspase-dependent cleavage of DDX21 suppresses host innate immunity

DEAD (Glu-Asp-Ala-Glu)-box RNA helicases have been proven to contribute to antiviral innate immunity. DDX21 RNA helicase was identified as a nuclear protein involved in ribosomal RNA processing and RNA unwinding. DDX21 was also proved to be the scaffold protein in the complex of DDX1-DDX21-DHX36 which senses double strand RNA and initiates downstream innate immunity. Here, we identified that DDX21 undergoes caspase-dependent cleavage after virus infection and treatment with RNA/DNA ligands, especially for RNA virus and ligands. Caspase-3/6 cleave DDX21 at D126 and promotes its translocation from the nucleus to the cytoplasm in response to virus infection. The cytoplasmic cleaved DDX21 negatively regulates the IFN-{beta} signaling pathway by suppressing the formation of DDX1-DDX21-DHX36 complex. Thus, our data identify DDX21 as a regulator of immune balance and most importantly uncover a potential role of DDX21 cleavage in the innate immunity response towards virus. ImportanceInnate immunity serves as the first barrier against virus infection. DEAD (Glu-Asp-Ala-Glu)-box RNA helicases, originally considered to be involved RNA processing and RNA unwinding, have been shown to play an important role in anti-viral innate immunity. The precise regulation of innate immunity is critical for the host because the aberrant production of cytokines leads to unexpected pathological consequences. Here, we identified DDX21 was cleaved at D126 by virus infection and treatment with RNA/DNA ligands via the caspase-3/6-dependent pathway. The cytoplasmic cleaved DDX21 negatively regulates the IFN-{beta} signaling pathway by suppressing the formation of DDX1-DDX21-DHX36 complex. In sum, our data identify DDX21 as a regulator of immune balance and most importantly uncover a potential role of DDX21 cleavage in the innate immunity response towards virus.

microbiology↗

bioRxiv2021

The Diameter Factor of Aligned Electrospinning Membranes Facilitates Cutaneous Wound Healing by Promoting Epithelialization

Topographical properties (such as pattern and diameter) of biomaterials play important roles in influencing cell activities and manipulating the related immune response during the skin wound healing. We prepared aligned electrospinning membranes with different fiber diameters including 319{+/-}100 nm (A300), 588{+/-}132 nm (A600) and 1048{+/-}130 nm (A1000). The A300 membranes significantly improved cell proliferation and spreading, and facilitated skin wound healing (epithelization and vascularization) with the regeneration of hair follicles. The transcriptome revealed the underlying molecular mechanism that A300 could promote macrophages transformation to reparative phenotypes with highly expressed IL10 and TGF{beta}, subsequently promoting epidermal cell migration via secreting matrix metalloproteinases 12 (MMP12). All the results indicate the A300 to be a potential candidate for guided skin regeneration applications. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/432929v3_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@17d754borg.highwire.dtl.DTLVardef@19fcb2forg.highwire.dtl.DTLVardef@1d4bc1eorg.highwire.dtl.DTLVardef@18a8091_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2021

Regeneration of spinal motor axons: Negative regulation by Celsr2 implicating Cdc42/Rac1 and JNK/c-Jun signaling

During development, cadherins Celsr2 and Celsr3 control axon navigation. Unlike Celsr3, Celsr2 remains expressed in the adult, suggesting unexplored roles in maintenance and repair. Here we show that Celsr2 knockdown promotes motor axon regeneration in mouse and human spinal cord explants and cultured motor neurons. Celsr2 downregulation is accompanied by increased levels of GTP-bound Rac1 and Cdc42, and of JNK and c-Jun proteins. Using a branchial plexus injury model, we show that forelimb functional recovery is improved in Celsr2 mutant versus control mice. Compared to controls, in mutant mice, reinnervated biceps muscles are less atrophic, contain more newly formed neuromuscular junctions, and generate larger electromyographic potentials, while motor neuron survival and axon regeneration are improved. GTP-bound Rac1 and Cdc42, JNK and c-Jun are upregulated in injured mutant versus control spinal cord. In conclusion, Celsr2 negatively regulates motor axon regeneration via Cdc42/Rac1/JNK/c-Jun signaling and is a target for neural repair.

neuroscience↗

bioRxiv2020

Real-time monitoring epidemic trends and key mutations in SARS-CoV-2 evolution by an automated tool

With the global epidemic of SARS-CoV-2, it is important to monitor the variation, haplotype subgroup epidemic trends and key mutations of SARS-CoV-2 over time effectively, which is of great significance to the development of new vaccines, the update of therapeutic drugs, and the improvement of detection reagents. The AutoVEM tool developed in the present study could complete all mutations detections, haplotypes classification, haplotype subgroup epidemic trends and key mutations analysis for 131,576 SARS-CoV-2 genome sequences in 18 hours on a 1 core CPU and 2G internal storage computer. Through haplotype subgroup epidemic trends analysis of 131,576 genome sequences, the great significance of the previous 4 specific sites (C241T, C3037T, C14408T and A23403G) was further revealed, and 6 new mutation sites of highly linked (T445C, C6286T, C22227T, G25563T, C26801G and G29645T) were discovered for the first time that might be related to the infectivity, pathogenicity or host adaptability of SARS-CoV-2. In brief, we proposed an integrative method and developed an efficient automated tool to monitor haplotype subgroup epidemic trends and screen out the key mutations in the evolution of SARS-CoV-2 over time for the first time, and all data could be updated quickly to track the prevalence of previous key mutations and new key mutations because of high efficiency of the tool. In addition, the idea of combinatorial analysis in the present study can also provide a reference for the mutation monitoring of other viruses.

genomics↗

bioRxiv2020

ORF3a mediated-incomplete autophagy facilitates SARS-CoV-2 replication

SARS-CoV-2 is the causative agent for the COVID-19 pandemic and there is an urgent need to understand the cellular response to SARS-CoV-2 infection. Beclin-1 is an essential scaffold autophagy protein that forms two distinct subcomplexes with modulators Atg14 and UVRAG, responsible for autophagosome formation and maturation, respectively. In the present study, we found that SARS-CoV-2 infection triggers an incomplete autophagy response, elevated autophagosome formation but impaired autophagosome maturation, and declined autophagy by genetic knockout of essential autophagic genes reduces SARS-CoV-2 replication efficiency. By screening 28 viral proteins of SARS-CoV-2, we demonstrated that expression of ORF3a alone is sufficient to induce incomplete autophagy. Mechanistically, SARS-CoV-2 ORF3a interacts with autophagy regulator UVRAG to facilitate Beclin-1-Vps34-Atg14 complex but selectively inhibit Beclin-1-Vps34-UVRAG complex. Interestingly, although SARS-CoV ORF3a shares 72.7% amino acid identity with the SARS-CoV-2 ORF3a, the former had no effect on cellular autophagy response. Thus, our findings provide the mechanistic evidence of possible takeover of host autophagy machinery by ORF3a to facilitate SARS-CoV-2 replication and raises the possibility of targeting the autophagic pathway for the treatment of COVID-19.

microbiology↗

bioRxiv2020

Cooperation-based sperm clusters mediate sperm oviduct entry and fertilization

Sperm cooperation has been observed in multiple species, yet its existence and benefit for reproductive success in mammals remains underexplored. Here, combining tissue-clearing with deep three-dimensional imaging, we demonstrate that postcopulatory mouse sperm congregate into unidirectional sperm cooperative clusters at the utero-tubal junction (UTJ), a key physical barrier for passage into the oviduct. Reducing sperm number in male mice by unilateral vasoligation or busulfan-treatment impairs sperm cluster formation and oviduct entry. Interestingly, sperm derived from Tex101-/- mouse has normal number, motility and morphology, yet they cannot form sperm cluster and fail to pass through the UTJ, which is at least in part due to the altered tail beating pattern of the Tex101-/- sperm. Moreover, Tex101-/- sperms defect in oviduct entry cannot be rescued by the presence of wild-type (WT) sperm in the same uteri by sequential mating, suggesting sperm cooperative cluster as an essential behavior contributing to male fertility, which could be related to human infertility or subfertility.

developmental biology↗

bioRxiv2020

Application of EGCG modified EDC/NHS cross-linked extracellular matrix to promote macrophage adhesion

Though chemically cross-linked by EDC/NHS endows collagen membrane with promising mechanical properties, it is not conducive to modulation of foreign body reaction (FBR) after implantation or guidance of osteogenesis. In our previous research, we have found that macrophages have a strong regulatory effect on tissue and bone regeneration during FBR, and EGCG modified membranes could adjust the recruitment and phenotypes of macrophages. Accordingly, we develop the EGCG-EDC/NHS membranes, prepared with physically immersion, while the surface morphology of the membrane was observed by SEM, the biological activity of collagen was determined by FTIR, the activity and adhesion of cell culture in vitro, angiogenesis and monocyte/macrophage recruitment after subcutaneous implantation, etc. are characterized. It could be concluded that EGCG-EDC/NHS collagen membrane is hopeful to be used in implant dentistry for it not only retains the advantages of the collagen membrane itself, but also improves cell viability, adhesion and vascularization tendency. However, the mechanism that lies in the regenerative advantages of such membrane needs further exploration, but it is certain that the differences in surface morphology can have a significant impact on the reaction between the host and the implant, not to mention macrophage in bone regeneration.

immunology↗

bioRxiv2020

Consideration of macrophage phenotypes under biomaterials mediated host defense process

Culturing macrophage in vitro is an important means to understand its reaction towards co-culture substances. However, the source of macrophages can be either purchased from specific cell line or extracted from bone marrow as differentiated macrophages. In order to assure the precision, when adopting extracted primary cell, screening in advance will be prominent before any processes to avoid results reserving that of non-macrophages. Here, we perform single-cell sequencing on open wound of skin in mice and focusing on the secreted proteins and surface markers related to traditional macrophage phenotypes (M1/M2) to ensure the importance of screening. The expression of CAMP when macrophages fight against candida albicans is another target to see its relationship with current classification. And results showed that identifying its phenotype without screening macrophages will far from the exact situation, and the expression of CAMP cannot be carried out by the traditional M1 and M2 macrophage. Thus, determining phenotype of macrophages based on function would be a promising way.

immunology↗

bioRxiv2020

Non-epigenetic mechanisms enable short memories of the environment for cell cycle commitment

Cells continuously survey their environment in order to make fundamental decisions, including whether to divide, migrate, or differentiate. However, a fascinating phenomenon in biology is that cells often possess memory--they temporally integrate both past and present signals to make a reliable decision. Cellular memory manifests across different biological systems over different timescales, and a variety of underlying molecular mechanisms have been proposed. Here we investigate a non-epigenetic molecular mechanism underpinning how a single yeast cell can remember its recent environmental history to decide whether to enter the cell cycle. This "memories" is encoded by the phosphorylation level of the cell cycle inhibitor Whi5. G1 cyclin Cln3 senses environmental nutrient levels and promotes cell-cycle entry by phosphorylating and thus inactivating Whi5. We developed an optogenetic system whereby the nuclear localization of Cln3 can be rapidly and reversibly controlled by light. By monitoring cellular response to different temporal profiles of Cln3, we found that cell cycle entry requires the time duration of nuclear Cln3, supporting the model of "cellular memories". Moreover, instead of the memory could last for the entire G1 phase as previously observed in glucose, we found Whi5 re-activates rapidly, with a similar half-time [~] 12 min, in a variety of nutrient and stress conditions. Our results suggest yeast cell can shortly remember its recent environmental cues to decide whether to enter the cell cycle.

molecular biology↗

bioRxiv2020

Antagonistic crosstalk fine-tunes sensitivities of IRE1 and PERK signaling during unfolded protein response

When endoplasmic reticulum (ER) stress occurs, a collection of phylogenetically conserved signaling pathways, termed unfolded protein response (UPR) pathways, monitors the stress level in the ER and is activated to restore homeostasis. If stress is overwhelming, activation of these signaling pathways also leads to apoptosis. The initial response in the ER is fluxed into several parallel branches, i.e., IRE1, PERK, and ATF6 branch. How they coordinate in response to different ER stress levels remains largely unknown. Here, we constructed a dual-reporter system to simultaneously monitor and quantify the response of both the IRE1 and PERK branches. We found that the IRE1 and PERK branches were highly coordinated via mutual inhibition. Furthermore, IRE1 branch was more sensitive to ER stress than the PERK branch under low ER stress and IRE1 activity was attenuated under high ER stress. The differential sensitivity between the two branches arises from the interbranch inhibitor p58IPK, rather than the intra-branch inhibitor GADD34. Our results suggested a model where cells use the antagonistic crosstalk between parallel UPR signaling pathways to fine-tune their activities in response to different ER stress levels.

cell biology↗

bioRxiv2020

ARG1 could be expressed by human, but not represent for repair

Arginase 1 (ARG1), typically expressed under stress or stimulation rather than in the healthy condition in humans. However, more and more studies claim ARG1 could be expressed by human and represents healing process. Including THP-1 monocyte shift to M2 macrophages rendered a higher expression of ARG1 than that with bone-graft has an ideal effect on anti-inflammation, resulting in tissue healing. With the higher expression of ARG1 seemingly induced by the constructed material and represented by the anti-inflammatory situation. For these reasons, this study focuses on whether traditional markers of macrophages could be express by human or not during clinical healing process. Through harvesting bone tissue samples during bone healing process and confirm the expression of markers at transcriptome and protein levels. The results showed the expression of ARG1 relatively low by bulk-RNA sequencing, quantitative polymerase chain reaction (qPCR), immunofluorescence (IF) and flow cytometry or could not be detected during process of healing of healthy donor. Taken together, results indicate that the ARG1 is not chosen for a regenerative marker in human bone tissue.

immunology↗

bioRxiv2020

Implementation-independent representation for deep convolutional neural networks and humans in processing faces

Deep convolutional neural networks (DCNN) nowadays can match and even outperform human performance in challenging complex tasks. However, it remains unknown whether DCNNs achieve human-like performance through human-like processes; that is, do DCNNs use similar internal representations to achieve the task as humans? Here we applied a reverse-correlation method to reconstruct the internal representations when DCNNs and human observers classified genders of faces. We found that human observers and a DCNN pre-trained for face identification, VGG-Face, showed high similarity between their "classification images" in gender classification, suggesting similar critical information utilized in this task. Further analyses showed that the similarity of the representations was mainly observed at low spatial frequencies, which are critical for gender classification in human studies. Importantly, the prior task experience, which the VGG-Face was pre-trained for processing faces at the subordinate level (i.e., identification) as humans do, seemed necessary for such representational similarity, because AlexNet, a DCNN pre-trained to process objects at the basic level (i.e., categorization), succeeded in gender classification but relied on a completely different representation. In sum, although DCNNs and humans rely on different sets of hardware to process faces, they can use a similar representation, possibly from similar prior task experiences, to achieve the same computation goal. Therefore, our study provides the first empirical evidence supporting the hypothesis of implementation-independent representation.

neuroscience↗

bioRxiv2020

Whi5 is diluted and protein synthesis does not dramatically increase in pre-Start G1

In their manuscript, Litsios et al.1 report a new model for how cell growth and biosynthetic activity control the G1/S transition in budding yeast. In essence, Litsios et al. claim that Start is driven by an increasing concentration of the G1 cyclin Cln3 due to a dramatic acceleration of protein synthesis in pre-Start G1 and not by the dilution of the cell cycle inhibitor Whi5. While we previously reported that Start was in part driven by cell growth during G1 diluting out the Start inhibitor Whi52, Litsios et al. report that Whi5 remains at constant concentration during G1, and changes in Whi5 concentration therefore do not contribute to Start. Since Litsios et al. directly contradict several key points of our own model of how cell growth triggers Start, we decided to investigate their claims and data. More specifically, we decided to investigate Litsios et al.s three major claims: O_LIWhi5 concentration remains constant during G1 C_LIO_LICln3 concentration strongly increases prior to Start C_LIO_LIGlobal protein synthesis rates increase by 2-3 fold prior to Start C_LI We investigated each of these three claims and found that the evidence presented by Litsios et al. does not support their claims due to inadequate analysis methods and flaws in their experiments.

molecular biology↗

bioRxiv2020

Virus-host interactome and proteomic survey of PMBCs from COVID-19 patients reveal potential virulence factors influencing SARS-CoV-2 pathogenesis

The ongoing coronavirus disease (COVID-19) pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a global public health concern due to relatively easy person-to-person transmission and the current lack of effective antiviral therapy. However, the exact molecular mechanisms of SARS-CoV-2 pathogenesis remain largely unknown. We exploited an integrated proteomics approach to systematically investigate intra-viral and virus-host interactomes for the identification of unrealized SARS-CoV-2 host targets and participation of cellular proteins in the response to viral infection using peripheral blood mononuclear cells (PBMCs) isolated from COVID-19 patients. Using this approach, we elucidated 251 host proteins targeted by SARS-CoV-2 and more than 200 host proteins that are significantly perturbed in COVID-19 derived PBMCs. From the interactome, we further identified that non-structural protein nsp9 and nsp10 interact with NKRF, a NF-[Kcy]B repressor, and may precipitate the strong IL-8/IL-6 mediated chemotaxis of neutrophils and overexuberant host inflammatory response observed in COVID-19 patients. Our integrative study not only presents a systematic examination of SARS-CoV-2-induced perturbation of host targets and cellular networks to reflect disease etiology, but also reveals insights into the mechanisms by which SARS-CoV-2 triggers cytokine storms and represents a powerful resource in the quest for therapeutic intervention.

microbiology↗

bioRxiv2020

Soybean Yellow Stripe-like7 is a symbiosome membrane peptide transporter essential for nitrogen fixation

Legumes form a symbiosis with rhizobia that convert atmospheric nitrogen (N2) to ammonia which they provide to the plant in return for a carbon and nutrient supply. Nodules, developed as part of the symbiosis, harbor rhizobia which are enclosed in the plant-derived symbiosome membrane (SM), to form a symbiosome. In the mature nodule all exchanges between the symbionts occur across the SM. Here we characterize GmYSL7, a member of Yellow stripe-like family which is localized to the SM in soybean nodules. It is expressed specifically in nodule infected cells with expression peaking soon after nitrogenase becomes active. Although most members of the family transport metal complexed with phytosiderophores, GmYSL7 does not. It transports oligopeptides of between four and 12 amino acids. Silencing of GmYSL7 reduces nitrogenase activity and blocks development when symbiosomes contain a single bacteroid. RNAseq of nodules in which GmYSL7 is silenced suggests that the plant initiates a defense response against the rhizobia. There is some evidence that metal transport in the nodules is dysregulated, with upregulation of genes encoding ferritin and vacuolar iron transporter family and downregulation of a gene encoding nicotianamine synthase. However, it is not clear whether the changes are a result of the reduction of nitrogen fixation and the requirement to store excess iron or an indication of a role of GmYSL7 in regulation of metal transport in the nodules. Further work to identify the physiological substrate for GmYSL7 will allow clarification of this role. One sentence summaryGmYSL7 is a symbiosome membrane peptide transporter that is essential for symbiotic nitrogen fixation that when silenced blocks symbiosome development.

plant biology↗

bioRxiv2020

Rhesus macaques can be effectively infected with SARS-CoV-2 via ocular conjunctival route

The outbreak of Corona Virus Disease 2019 caused by the severe acute respiratory syndrome coronavirus (SARS-CoV-2) is highly transmitted. The potential extra-respiratory transmission routes remain uncertain. Five rhesus macaques were inoculated with 1x106 TCID50 of SARS-CoV-2 via conjunctival (CJ), intratracheal (IT), and intragastric (IG) routes, respectively. Remarkably, the CJ inoculated-macaques developed mild interstitial pneumonia and viral load was detectable in the conjunctival swabs at 1 days post-inoculation (dpi). Only via IT inoculation, viral load was detected in the anal swab at 1-7 dpi and macaque showed weight loss. However, viral load was undetectable after IG inoculation. Comparatively, viral load was higher in the nasolacrimal system but lesions of lung were relatively mild and local via CJ inoculation compared with that via IT inoculation, demonstrating distinct characteristics of virus dispersion. Both the two routes affected the alimentary tract. Therefore the clinicians need to protect eye while working with patients.

microbiology↗

bioRxiv2020

Reinfection could not occur in SARS-CoV-2 infected rhesus macaques

A global pandemic of Corona Virus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome CoV-2 (SARS-CoV-2) is ongoing spread. It remains unclear whether the convalescing patients have a risk of reinfection. Rhesus macaques were rechallenged with SARS-CoV-2 during an early recovery phase from initial infection characterized by weight loss, interstitial pneumonia and systemic viral dissemination mainly in respiratory and gastrointestinal tracts. The monkeys rechallenged with the identical SARS-CoV-2 strain have failed to produce detectable viral dissemination, clinical manifestations and histopathological changes. A notably enhanced neutralizing antibody response might contribute the protection of rhesus macaques from the reinfection by SARS-CoV-2. Our results indicated that primary SARS-CoV-2 infection protects from subsequent reinfection. One Sentence SummaryNeutralizing antibodies against SARS-CoV-2 might protect rhesus macaques which have undergone an initial infection from reinfection during early recovery days.

microbiology↗