Biology subjects

Li, Q.

Publications and source records attributed to Li, Q..

At least 577 records · Page 32Linked to original sources

bioRxiv2021

Immunological profiling of COVID-19 patients with pulmonary sequelae

Cellular immunity may be involved in organ damage and rehabilitation in patients with coronavirus disease 2019 (COVID-19). We aimed to delineate immunological features of COVID-19 patients with pulmonary sequelae (PS) one year after discharge. 50 COVID-19 survivors were recruited and classified according to radiological characteristics: 24 patients with PS and 26 patients without PS. Phenotypic and functional characteristics of immune cells were evaluated by multiparametric flow cytometry. Patients with PS had an increased proportion of natural killer (NK) cells and lower percentage of B cells compared to patients without PS. Phenotypic and functional features of T cells in patients with PS were predominated by the accumulation of CD4+ T cells secreting IL-17A, short-lived effector-like CD8+ T cells (CD27-CD62L-) and senescent T cells with excessive secretion of granzyme-B/perforin/IFN-{gamma}. NK cells were characterized by the excessive secretion of granzyme-B and perforin and the downregulation of NKP30 and NKP46; highly activated NKT and {gamma}{delta} T cells exhibited NKP30 and TIM-3 upregulation and NKB1 downregulation in patients with PS. However, immunosuppressive cells were comparable between the two groups. The interrelation of immune cells in COVID-19 was intrinsically identified, whereby T cells secreting IL-2, IL-4 and IL-17A were enriched among CD28+ and CD57-cells and cells secreting perforin/granzyme-B/IFN-{gamma}/TNF- expressed markers of terminal differentiation. CD57+NK cells, CD4+perforin+ T cells and CD8+CD27+CD62L+ T cells were identified as the independent predictors for residual lesions. Overall, our findings unveil the profound imbalance of immune landscape that may correlate with organ damage and rehabilitation in COVID-19. IMPORTANCEA considerable proportion of COVID-19 survivors have residual lung lesions, such as ground glass opacity and fiber streak shadow. To determine the relationship between host immunity and residual lung lesions, we performed an extensive analysis of immune responses in convalescent patients with COVID-19 one year after discharge. We found significant differences in immunological characteristics between patients with pulmonary sequelae and patients without pulmonary sequelae one year after discharge. Our study highlights the profound imbalance of immune landscape in the COVID-19 patients with pulmonary sequelae, characterized by the robust activation of cytotoxic T cells, NK cells and {gamma}{delta} T cells as well as the deficiencies of immunosuppressive cells. Importantly, CD57+NK cells, CD4+perforin+ T cells and CD8+CD27+CD62L+ T cells were identified as the independent predictors for residual lesions.

immunology↗

bioRxiv2021

Partial genome assembly of the medicinal plant Ephedra sinica.

Ephedra sinica is a high-value medicinal plant that produces important phenylpropylamino alkaloids pseudoephedrine and ephedrine. Few genomics resources exist for E. sinica, which has been characterized as a tetraploid with a monoploid genome size of 8.56 Gb. Here we reported a partial genome assembly of E. sinica (12.8 Gb) based on Illumina short-read sequencing at low coverage.

genomics↗

bioRxiv2021

Extraction, purification and anti-TMV effects of α (β)-2,7,11-cembratriene-4,6-diol from tobacco leaves

BackgroundAcetone ethanol extracts from tobacco leaves have antiviral activity against TMV, but the antiviral effects of their specialized metabolites have not been systematically studied yet, especially the underlying mechanism is still unexplored. ResultsThe tobacco cembranoids ({beta})-2,7,11-cembratriene-4,6-diol (({beta})-CBD) were extracted and purified with an effective and green protocol including innovatively added 5% phosphoric acid for elution, one time silica gel chromatographic column separation and impurity removal and further HPLC purification. The results of antiviral activities against tobacco mosaic virus (TMV) with the local lesion counting method showed that ({beta})-CBD have in vivo higher protective effects of 73.2% and 71.6%, at 75.0 M, respectively, than control agent Ningnanmycin (53.1%). Notably, The results of ELISA and and TMV-GFP fluorescent optical imaging assay indicated a obviously reduced viral protein and weaker GFP fluorescence signal and smaller infection area, which confirmed their anti-TMV activities at protein level. Furthermore, the enhanced production of SA and JA and the significantly increased transcription of of JA signaling pathway (COI1 and PDF1.2) and SA signaling pathway genes (PR1, NPR1 and EDS1) in treated plants further conformed that exogenously applied ({beta})-CBD can effectively elicit the tobacco plant immunity against TMV. ConclusionsThe ({beta})-CBD mainly stimulates disease resistance of tobacco plants to resist TMV and it can be used as bioagents to control TMV in the future.

plant biology↗

bioRxiv2021

Distinct Brain Mechanisms for Conflict Adaptation Within and Across Conflict Types

Cognitive conflict, like other cognitive processes, shows the characteristic of adaptation, i.e., conflict effects are attenuated when immediately following a conflicting event, a phenomenon known as the conflict adaptation effect (CAE). One important aspect of CAE is its sensitivity to the intertrial coherence of conflict type, i.e., behavioral CAE occurs only if consecutive trials are of the same conflict type. Although reliably observed behaviorally, the neural mechanisms underlying such a phenomenon remains elusive. With a paradigm combining the classic Simon task and Stroop task, this fMRI study examined neural correlates of conflict adaptation both within and across conflict types. The results revealed that when the conflict type repeated (but not when it alternated), the CAE-like neural activations were observed in dorsal anterior cingulate cortex, inferior frontal gyrus, superior parietal lobe, etc. (i.e., regions within typical task-positive networks). In contrast, when the conflict type alternated (but not when it repeated), we found CAE-like neural deactivations in a range of regions including bilateral superior and medial frontal gyri, bilateral angular cortex, bilateral temporal cortices, etc. (i.e., regions within the typical task-negative network). Moreover, this CAE-like neural deactivation predicts behavior performance. Network analyses suggested that these regions (for CAE-like neural activities within and across conflict type[s] respectively) can be clustered into two antagonistic networks. This evidence suggests that our adaptation to cognitive conflicts within a conflict type and across different types may rely on these two distinct neural mechanisms.

neuroscience↗

bioRxiv2021

Competition between distinct ApoE alleles and mCRP for the endothelial receptor CD31 differentially regulates neurovascular inflammation and Alzheimer's disease pathology

BACKGROUNDC-reactive protein (CRP) in peripheral inflammation is associated with increased Alzheimers disease (AD) risk in Apolipoprotein E4 (ApoE4), but not ApoE3 or E2, humans. It remains unknown whether peripheral monomeric CRP (mCRP) induces AD pathogenesis through some receptor of blood-facing endothelia in the brain in an ApoE genotype dependent fashion. METHODSWe used human samples, ApoE knock-in and deficient mouse models, and primary brain endothelia. Different ApoE mice were intraperitoneally (i.p.) injected with mCRP. The characterizations by immunostaining, proximity ligation assay (PLA) and siRNA were conducted to identify the receptor for mCRP. Brain microvessel and endothelia were isolated for RNA sequencing to explore the molecular pathway. RESULTSWe demonstrate that CD31 (PECAM-1), a blood-facing endothelial receptor in brain, is a competitive target of both mCRP and ApoE protein. ApoE2 competes more strongly with mCRP for CD31 than ApoE4 does, and expressing ApoE4 or knocking out ApoE gene results in higher levels of mCRP-CD31 binding, leading to a decrease of CD31 expression but an increase in CD31 phosphorylation, along with greater cerebrovascular damage and AD pathology. This competitive binding mediates differential endothelial molecular responses depending on ApoE genotype, increasing cerebrovascular inflammation and mitochondria impairment in ApoE4 mice, while inducing vasculogenesis and protective changes in the presence of ApoE2. CONCLUSIONSOur study reveals a novel and dynamic endothelial ApoE-mCRP-CD31 pathway for AD pathogenesis during chronic inflammation and provides some insight into the opposing ApoE4-neurodegenerative and ApoE2-neuroprotective effects in AD. Clinical PerspectiveO_ST_ABSWHAT IS NEW?C_ST_ABSO_LICD31 is a competitive target of both mCRP and ApoE in brain endothelia in an ApoE-allele dependent pattern C_LIO_LImCRP increases CD31 phosphorylation in the brain endothelia and damages cerebrovasculature in ApoE4 carriers and AD brains C_LIO_LImCRP expression results in neuroprotective or neurodegenerative pathway activation in an ApoE-dependent manner C_LI WHAT ARE THE CLINICAL IMPLICATIONS?O_LIAlthough ApoE4 is a major genetic risk factor of AD, some ApoE4 carriers do not develop AD by the age of 90. C_LIO_LIElderly people often experience peripheral inflammatory attacks and develop chronic low-grade inflammation, which results in the formation and release of mCRP. Because CRP is routine clinical laboratory test, clinicians can use blood CRP level to predict AD risk in ApoE4 carriers. C_LIO_LIEvidence of Apoe4 genotype and chronic low-grade inflammation stages marked by elevated CRP levels should be targeted in personalized treatment and clinical trials for AD. C_LI

neuroscience↗

bioRxiv2021

Modelling, Analysis, and Optimization of Three-Dimensional Restricted Visual Field Metric-Free Swarms

Models of collective behaviour have been proved helpful in revealing what mechanism may underlie characteristics of a flock of birds, a school of fish, and a swarm of herds. Recently, the metric-free model gradually occupies a dominant position in the research field of collective intelligence. Most of these models endow every single individual with the ability of a global visual field, which can offer each particle sufficient external information. In this paper, we mainly focus on whether the global visual field is necessary to form a consistent and cohesive group or not. Inspired by the biological characteristic of starlings, we develop a three-dimensional restricted visual field metric-free(RVFMF) model based on Pearce and Turners previous work. We further investigate several vital factors governing the convergent consistency of the RVFMF model with the assistance of extensive numerical simulations. According to the simulation results, we conclude that the best view angle of each particle in a swarm increases with the expansion of the population size. Besides, the best view angle gradually becomes stable around 155 degrees when the population size is larger than 1000. We also offer quantitative analysis data to prove that a flock of birds could obtain better consistency under optimal restricted visual field than under global visual field.

biophysics↗

bioRxiv2021

The endoplasmic reticulum associated degradation adaptor Sel1L regulates T cell homeostasis and function

Suppressor/Enhancer of Lin-12-like (Sel1L) is a critical adaptor for endoplasmic reticulum-associated degradation (ERAD), a process that maintains cellular protein quality control through degradation of misfolded proteins. Here we investigate the role of Sel1L in T cell homeostasis and function. T cell-specific deletion of Sel1L profoundly impairs peripheral T cell survival and promotes apoptotic cell death. Furthermore, Sel1L is required to maintain naive CD8+ T cell homeostasis in a cell-intrinsic manner with loss of quiescence as evidenced by increased proliferation. Sel1L-deficient T cells exhibit enhanced activation of the mammalian target of rapamycin (mTOR) pathway and altered cellular metabolism, including increased cellular reactive oxygen species, mitochondrial mass and mitochondrial membrane potential in the naive CD8+ T cell compartment. Furthermore, loss of Sel1L impaired CD8+ T cell immune responses following bacterial infection. These results demonstrate a novel role for Sel1L/ERAD in T cell homeostasis and function.

immunology↗

bioRxiv2021

TLR2 on CD4+ and CD8+ T cells promotes late control of Mycobacterium tuberculosis infection

Although a role for TLR2 on T cells has been indicated in prior studies, in vivo stimulation of TLR2 on T cells by Mtb and its impact on Mtb infection has not been tested. Furthermore, it is not known if the enhanced susceptibility to Mtb of Tlr2 gene knockout (ko) mice is due to its role in macrophages, on T cells or both. To address TLR2 on T cells, we generated Tlr2fl/flxCd4cre/cre mice, which lack expression of TLR2 on both CD4 and CD8 T cells, to study the in vivo role of TLR2 on T cells after aerosol infection with virulent Mtb. Deletion of TLR2 in CD4+ and CD8+ T cells reduces their ability to be co-stimulated by TLR2 ligands for cytokine production. These include both pro-(IFN-{gamma}, TNF-) and anti-inflammatory cytokines (IL-10). Deletion of TLR2 in T cells did not affect early control but did result in decreased late control of Mtb in the lungs of infected mice. This suggests that T cell co-stimulation by mycobacterial TLR2 ligands in vivo is important for control of infection during the chronic phase of Mtb infection in the lung.

immunology↗

bioRxiv2021

Edaravone activates the GDNF/RET neurotrophic signaling pathway and protects mRNA-induced motor neurons from iPS cells.

BackgroundSpinal cord motor neurons (MNs) from human iPS cells (iPSCs) have wide applications in disease modeling and therapeutic development for amyotrophic lateral sclerosis (ALS) and other MN-associated neurodegenerative diseases. We need highly efficient MN differentiation strategies for generating iPSC-derived disease models that closely recapitulate the genetic and phenotypic complexity of ALS. An important application of these models is to understand molecular mechanisms of action of FDA-approved ALS drugs that only show modest clinical efficacy. Novel mechanistic insights will help us design optimal therapeutic strategies together with predictive biomarkers to achieve better efficacy. MethodsWe induce efficient MN differentiation from iPSCs in 4 days using synthetic mRNAs coding two transcription factors (Ngn2 and Olig2) with phosphosite modification. These MNs after extensive characterization were applied in electrophysiological and neurotoxicity assays as well as transcriptomic analysis, to study the neuroprotective effect and molecular mechanisms of edaravone, an FDA-approved drug for ALS, for improving its clinical efficacy. ResultsWe generate highly pure and functional mRNA-induced MNs (miMNs) from normal and ALS iPSCs, as well as embryonic stem cells. Edaravone alleviates H2O2-induced neurotoxicity and electrophysiological dysfunction in miMNs, demonstrating its neuroprotective effect that was also found in the glutamate-induced miMN neurotoxicity model. Guided by the transcriptomic analysis, we show a previously unrecognized effect of edaravone to induce the GDNF receptor RET and the GDNF/RET neurotrophic signaling in vitro and in vivo, suggesting a clinically translatable strategy to activate this key neuroprotective signaling. Notably, edaravone can replace required neurotrophic factors (BDNF and GDNF) to support long-term miMN survival and maturation, further supporting the neurotrophic function of edaravone-activated signaling. Furthermore, we show that edaravone and GDNF combined treatment more effectively protects miMNs from H2O2-induced neurotoxicity than single treatment, suggesting a potential combination strategy for ALS treatment. ConclusionsThis study provides methodology to facilitate iPSC differentiation and disease modeling. Our discoveries will facilitate the development of optimal edaravone-based therapies for ALS and potentially other neurodegenerative diseases. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/443325v2_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@cd0bc9org.highwire.dtl.DTLVardef@1c0c0b6org.highwire.dtl.DTLVardef@1ac0952org.highwire.dtl.DTLVardef@1980f5b_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2021

Somatic genetics analysis of sleep in adult mice

Classical forward and reverse mouse genetics approaches require germline mutations and, thus, are unwieldy to study sleep functions of essential genes or redundant pathways. It is also time-consuming to conduct electroencephalogram/electromyogram-based mouse sleep screening owning to labor-intensive surgeries and genetic crosses. Here, we describe a highly accurate SleepV (video) system and adeno-associated virus (AAV)-based adult brain chimeric (ABC)- expression/knockout (KO) platform for somatic genetics analysis of sleep in adult mice. A pilot ABC-expression screen identifies CREB and CRTC1, of which constitutive or inducible expression significantly reduces quantity and quality of non-rapid eye movement sleep. Whereas ABC-KO of exon 13 of Sik3 by AAV-Cre injection in Sik3-E13flox/flox adult mice phenocopies Sleepy (Sik3Slp/+) mice, ABC-CRISPR of Slp/Sik3 reverses hypersomnia of Sleepy mice, indicating a direct role of SLP/SIK3 kinase in sleep regulation. Multiplex ABC-CRISPR of both orexin/hypocretin receptors causes narcolepsy-like episodes, enabling one-step analysis of redundant genes in adult mice. Finally, ABC-expression/KO screen identifies Ankrd63 and NR1 as two potentially new sleep regulators. Therefore, this somatic genetics approach should facilitate high-throughput analysis of sleep regulatory genes, especially for essential or redundant genes, in adult mice by skipping the mouse development and genetic crosses.

neuroscience↗

bioRxiv2021

Effects of short-term plasticity in early olfactory information processing in Drosophila

In Drosophila, olfactory information received by the olfactory receptor neurons (ORNs) is first processed by an incoherent feed forward neural circuit in the antennal lobe (AL) that consists of ORNs (input), the inhibitory local neurons (LNs), and projection neurons (PNs). This "early" olfactory information process has two important characteristics. First, response of a PN to its cognate ORN is normalized by the overall activity of other ORNs, a phenomenon termed "divisive normalization". Second, PNs respond strongly to the onset of ORN activities, but they adapt to prolonged or continuously increasing inputs. Despite the importance of these characteristics for learning and memory, their underlying mechanism remains not fully understood. Here, we develop a circuit model for describing the ORN-LN-PN dynamics by including key features of neuron-neuron interactions, in particular short-term plasticity (STP) and presynaptic inhibition (PI). Our model shows that STP is critical in shaping PNs steady-state response properties. By fitting our model to experimental data quantitatively, we found that strong and balanced short-term facilitation (STF) and short-term depression (STD) in STP is crucial for the observed nonlinear divisive normalization in Drosophila. By comparing our model with the observed adaptive response to time-varying signals quantitatively, we find that both STP and PI contribute to the highly adaptive response with the latter being the dominant factor for a better fit with experimental data. Our model not only helps reveal the mechanisms underlying two main characteristics of the early olfactory process, it can also be used to predict the PN responses to arbitrary time-dependent signals and to infer microscopic properties of the circuit (such as the strengths of STF and STD) from the measured input-output relation.

neuroscience↗

bioRxiv2021

DNA methylation affects pre-mRNA transcriptional initiation and processing in Arabidopsis

BackgroundDNA methylation may regulate pre-mRNA transcriptional initiation and processing, thus affecting gene expression. Unlike animal cells, plants, especially Arabidopsis thaliana, have relatively low DNA methylation levels, limiting our ability to observe any correlation between DNA methylation and pre-mRNA processing using typical short-read sequencing. However, with newly developed long-read sequencing technologies, such as Oxford Nanopore Technology Direct RNA sequencing (ONT DRS), combined with whole-genome bisulfite sequencing, we were able to precisely analyze the relationship between DNA methylation and pre-mRNA transcriptional initiation and processing using DNA methylation-related mutants. ResultsUsing ONT DRS, we generated more than 2 million high-quality full-length long reads of native mRNA for each of the wild type Col-0 and mutants defective in DNA methylation, identifying a total of 117,474 isoforms. We found that low DNA methylation levels around splicing sites tended to prevent splicing events from occurring. The lengths of the poly(A) tail of mRNAs were positively correlated with DNA methylation. DNA methylation before transcription start sites or around transcription termination sites tended to result in gene-silencing or read-through events. Furthermore, using ONT DRS, we identified novel transcripts that we could not have otherwise, since transcripts with intron retention and fusion transcripts containing the uncut intergenic sequence tend not to be exported to the cytoplasm. Using the met1-3 mutant with activated constitutive heterochromatin regions, we confirmed the effects of DNA methylation on pre-mRNA processing. ConclusionThe combination of ONT DRS with whole-genome bisulfite sequencing was a powerful tool for studying the effects of DNA methylation on splicing site selection and pre-mRNA processing, and therefore regulation of gene expression.

plant biology↗

bioRxiv2021

Tetratricopeptide repeat domain 36 protects renal tubular cells from cisplatin-induced apoptosis via maintaining mitochondrial homeostasis

The apoptosis of proximal tubule epithelial cells (PTECs) is a critical event of acute kidney injury (AKI). Tetratricopeptide repeat domain 36 (TTC36) with three tetratricopeptide repeats is evolutionarily conserved across mammals, which functions as a chaperone for heat shock protein 70. We have revealed that TTC36 is specifically expressed in PTECs in our previous work. There are few studies about the role TTC36 played in AKI. Therefore, in this study, we investigated the function of TTC36 in the apoptosis of HK2 cells, which are derived from the human proximal tubule. Firstly, we observed that TTC36 was obviously down-regulated and was negatively related to the kidney damage degree in a mouse model of acute kidney injury established by ischemia/reperfusion. In addition, TTC36 overexpression protected HK2 cells against cisplatin-induced apoptosis. Moreover, we discovered the mechanism that TTC36 mitigated cisplatin-triggered mitochondrial disorder via sustaining the membrane potential of mitochondria and mitochondrial autophagy-related gene expression. Collectively, these results suggested that TTC36 plays a protective role in the cisplatin-induced apoptosis of renal tubular cells through maintaining the mitochondrial potential and mitochondrial autophagy-related gene expression. These observations highlight the essential role of TTC36 in regulating PTEC apoptosis and imply TTC36/mitochondrial homeostasis axis as a potential target for the therapeutic intervention in AKI.

cell biology↗

bioRxiv2021

In situ electro-sequencing in three-dimensional tissues

Pairwise mapping of single-cell gene expression and electrophysiology in intact three-dimensional (3D) tissues is crucial for studying electrogenic organs (e.g., brain and heart)1-5. Here, we introduce in situ electro-sequencing (electro-seq), combining soft bioelectronics with in situ RNA sequencing to stably map millisecond-timescale cellular electrophysiology and simultaneously profile a large number of genes at single-cell level across 3D tissues. We applied in situ electro-seq to 3D human induced pluripotent stem cell-derived cardiomyocyte (hiPSC-CM) patches, precisely registering the CM gene expression with electrophysiology at single-cell level, enabling multimodal in situ analysis. Such multimodal data integration substantially improved the dissection of cell types and the reconstruction of developmental trajectory from spatially heterogeneous tissues. Using machine learning (ML)-based cross-modal analysis, in situ electro-seq identified the gene-to-electrophysiology relationship over the time course of cardiac maturation. Further leveraging such a relationship to train a coupled autoencoder, we demonstrated the prediction of single-cell gene expression profile evolution using long-term electrical measurement from the same cardiac patch or 3D millimeter-scale cardiac organoids. As exemplified by cardiac tissue maturation, in situ electro-seq will be broadly applicable to create spatiotemporal multimodal maps and predictive models in electrogenic organs, allowing discovery of cell types and gene programs responsible for electrophysiological function and dysfunction.

genomics↗

bioRxiv2021

Genome-wide CRISPR activation screen identifies novel receptors for SARS-CoV-2 entry

The ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been endangering worldwide public health and economy. SARS-CoV-2 infects a variety of tissues where the known receptor ACE2 is low or almost absent, suggesting the existence of alternative pathways for virus entry. Here, we performed a genome-wide barcoded-CRISPRa screen to identify novel host factors that enable SARS-CoV-2 infection. In addition to known host proteins, i.e. ACE2, TMPRSS2 and NRP1, we identified multiple host components, among which LDLRAD3, TMEM30A and CLEC4G were confirmed as functional receptors for SARS-CoV-2. All these membrane proteins bind directly to spikes N-terminal domain (NTD). Their essential and physiological roles have all been confirmed in either neuron or liver cells. In particular, LDLRAD3 and CLEC4G mediate SARS-CoV-2 entry and infection in a fashion independent of ACE2. The identification of the novel receptors and entry mechanisms could advance our understanding of the multiorgan tropism of SARS-CoV-2, and may shed light on the development of the therapeutic countermeasures against COVID-19.

microbiology↗

bioRxiv2021

Transcriptome analysis reveals regulatory networks and hub genes in flavonoid metabolism of Rosa roxburghii

Rosa roxburghii Tratt, the most popular fruit that blooms in the southwest of China, is rich in flavonoids. However, the regulatory network and critical genes involved in the metabolism of flavonoid compounds in R. roxburghii are still unknown. In this study, we revealed that flavonoid, anthocyanin and catechin accumulated at different levels in various tissues of R. roxburghii. We further obtained and analyzed differentially expressed genes (DEGs) involved in flavonoid metabolism from five samples of R. roxburghii by transcriptome sequencing. A total of 1 130 DEGs were identified, including 166 flavonoid pathway biosynthesis genes, 622 transcription factors, 301 transporters, and 221 cytochrome P450 proteins. A weighted gene co-expression network analysis (WGCNA) of the DEGs uncovered different co-expression networks. In terms of biosynthesis enzymes, cytochrome P450 CYP749A22 and CYP72A219 were highlighted in regulation flavonoids content. Anthocyanin 3-O-glucosyltransferase and F3H were the top two critical enzymes for anthocyanin content. In contrast, caffeic acid 3-O-methyltransferase, 4-coumarate-CoA ligase, and shikimate O-hydroxycinnamoyl transferase were essential for catechin accumulation. Additionally, the eigengene network of the "black" module had high correlations with total flavonoid (r= 0.9, p=5e-06). There were 26 eigengenes in the "black" module, including six flavonoid biosynthesis, 14 TFs and six transporters. Among them, besides cytochrome P450 proteins (DN136557_c0_g1, DN135573_c0_g1 and DN145971_c4_g1), isoflavone-hydroxylase (DN143321_c3_g1) was crucial for total flavonoids content based on the high degree of connectivity. The transcription factors RrWRKY45 (DN142829_c1_g5), RrTCP20 (DN146443_c1_g1) and RrERF118 (DN141507_c3_g2) were significantly correlated with flavonoids in R. roxburghii. The present transcriptomic and biochemical data on metabolites should encourage further investigation on functional genomics and breeding of R. roxburghii with strong pharmaceutical potential.

plant biology↗

bioRxiv2021

Epigallocatechin Gallate from Green Tea Effectively Blocks Infection of SARS-CoV-2 and New Variants by Inhibiting Spike Binding to ACE2 Receptor

As the COVID-19 pandemic rages on, the new SARS-CoV-2 variants have emerged in the different regions of the world. These newly emerged variants have mutations in their spike (S) protein that may confer resistance to vaccine-elicited immunity and existing neutralizing antibody therapeutics. Therefore, there is still an urgent need of safe, effective, and affordable agents for prevention/treatment of SARS-CoV-2 and its variant infection. Here, we demonstrated that green tea beverage (GTB) or its major ingredient, epigallocatechin gallate (EGCG), were highly effective in inhibiting infection of live SARS-CoV-2 and human coronavirus (HCoV OC43). In addition, infection of the pseudoviruses with spikes of the new variants (UK-B.1.1.7, SA-B.1.351, and CA-B.1.429) was efficiently blocked by GTB or EGCG. Among the 4 active green tea catechins at noncytotoxic doses, EGCG was the most potent in the action against the viruses. The highest inhibitory activity was observed when the viruses or the cells were pre-incubated with EGCG prior to the infection. Mechanistic studies revealed that EGCG blocked infection at the entry step through interfering with the engagement of the receptor binding domain (RBD) of the viral spikes to angiotensin-converting enzyme 2 (ACE2) receptor of the host cells. These data support further clinical evaluation and development of EGCG as a novel, safe, and cost-effective natural product for prevention/treatment of SARS-CoV-2 transmission and infection.

microbiology↗

bioRxiv2021

Hydroxyl-radical scavenging activity of hydrogen does not significantly contribute to its biological function

Since Ohsawa et al. reported a biological antioxidant function of hydrogen in 2007, researchers have now shown it to exert protective effects in a wide range of human and animal disease models. Clinical observations and scientific arguments suggest that a selective scavenging property of H2 cannot adequately explain the beneficial effects of hydrogen. However, there is no experiment challenging the original published data, which suggested that molecular hydrogen dissolved in solution reacts with hydroxyl radicals in cell-free systems. Here we report that a hydrogen-saturated solution (0.6 mM) did not significantly reduce hydroxyl radicals in the Fenton system using 1 mM H2O2. We replicated the same condition as Ohsawas study (i.e. 5 {micro}M H2O2), and observed a decrease in *OH radicals in both the H2-rich and N2-rich solutions, which may be caused by a decreased dissolved oxygen concentration. Finally, we determined the effect of hydrogen on a high-valence iron enzyme, horseradish peroxidase (HRP), and found that hydrogen could directly increase HRP activity in a dose-dependent manner. Overall, these results indicate that although H2 and *OH can react, the reaction rate is too low to have physiological function. The target of hydrogen is more complex, and its interaction with enzymes or other macro-molecules deserve more attention and in-depth study.

biochemistry↗