Biology subjects

Jiang, H.

Publications and source records attributed to Jiang, H..

At least 289 records · Page 16Linked to original sources

bioRxiv2020

Sequencing of clinical samples reveals that adaptation keeps establishing during H7N9 virus infection in humans

The H7 subtype avian influenza viruses (AIV) have a much longer history and their adaptation through evolution pose continuous threat to humans 1. Since 2013 March, the novel reasserted H7N9 subtype have transmitted to humans through their repeated assertion in the poultry market. Through repeated transmission, H7N9 gradually became the second AIV subtype posing greater public health risk after H5N1 2,3. After infection, how the virus tunes its genome to adapt and evolve in humans remains unknown. Through direct amplification of H7N9 and high throughput (HT) sequencing of full genomes from the swabs and lower respiratory tract samples collected from infected patients in Shenzhen, China, we have analyzed the in vivo H7N9 mutations at the level of whole genomes and have compared with the genomes derived by in vitro cultures. These comparisons and frequency analysis against the H7N9 genomes in the public database, 40 amino acids were identified that play potential roles in virus adaptation during H7N9 infection in humans. Various synonymous mutations were also identified that might be crucial to H7N9 adaptation in humans. The mechanism of these mutations occurred in a single infection are discussed in this study.

microbiology↗

bioRxiv2020

High-resolution Cell Atlas of Pig Lung and Online Platform Exploring for Lung Single Cell

Due to the comparable organ sizes and physiology to human beings, genetically engineered pig is gradually regarded as an optimal source of human for transplantation and an excellent model for human diseases research. The major barrier between pig and human is mainly cellular heterogeneity and immune incompatibilities. Myriad scRNA-seq data of human has been reported, but the counterpart in pig is scarce. Here, we applied scRNA-seq technology to study the cellular heterogeneity of 3 months old pig lungs, generating the single-cell atlas of 13,580 cells covering 16 major cell types. Based on this data, we systematically characterized transcription factor regulatory networks, cell-cell communications in each cell type, and comparison of them and those in human lung. We first presented a comprehensive and openly accessible online platform, ScdbLung, which was composed of three functional modules (Marker, Cluster, and Download) and dedicated to exploiting the valuable resources of lung scRNA-seq data across four mammalian species. Overall, our scRNA-seq atlas of domestic pig lung, conserved transcription factor regulatory networks and cell-cell communications between domestic pig and human, and ScdbLung could provide guidance for porcine lung research and clinical applicability.

cell biology↗

bioRxiv2020

Longest Order Conserved Exemplar Subsequences

We propose a new problem whose input data are two linear genomes together with two indexed gene subsequences of them, which asks to find a longest common exemplar subsequence of the two given genomes with a subsequence identical to the given indexed gene subsequences. We present an algorithm for this problem such that the algorithm is allowed to take diminishing time and space to solve the problem by setting the indexed genes with an incremental number. Although an incremental number of indexed genes were selected, the algorithm was verified definite to reach a solution whose length insistently comes very close to a real longest common exemplar subsequence of the two given genomes. Aiming at 23 human/gorilla chromosome pairs, the algorithm was examined for use in questing for longest common exemplar subsequences whose basic units are annotated genes as well as pseudo genes, namely consecutive DNA subsequences. By contrasting the pseudo gene common exemplar subsequences the algorithm had reached for the human chromosomes 7 and 16 and their gorilla homologues with those annotated genes in the human and gorilla chromosomes, we found more than 1 000 and 500 pseudo genes in the human chromosomes 7 and 16 that occur in the same order as they are in the gorilla chromosomes 7 and 16 and, do not overlap with any annotated gene. Author summaryThere is a benefit of the algorithm: It can reach a long enough common exemplar subsequence of two linear genomes in as fast a speed as one requires even if the given genomes would be equipped with too many duplicated genes, which can be done by setting incremental number of indexed genes. We developed a Java software based on the algorithm, that has been available for download on https://github.com/ShuZhang-sdu/LCES. Only in need to set the indexed gene sequences as null, was it verified successful for our algorithm to obtain the longest common exemplar subsequences of the annotated gene summary pairs extracted from 23 human/gorilla chromosome pairs. In convenience for researchers to find new motifs or conserved genes, we devoted for the algorithm to quest pseudo gene (i.e. consecutive DNA subsequences) summary pairs of the 23 human/gorilla chromosome pairs for solutions. There are 20 pseudo gene summary pairs whose longest common exemplar subsequences have been found by the algorithm with null indexed gene sequences. The other 3 pseudo gene summary pairs were verified solvable for the algorithm to reach their longest common exemplar subsequences that have to admit subsequences identical to given indexed gene subsequences. There were informed to exist 2 353 and 1 148 pseudo genes in the gorilla chromosome 7 and 16 that occur in the same order as they are in the human chromosome 7 and 16 and, do not overlap with any annotated gene. These pseudo genes should be significant for annotating the human or gorilla genome.

bioinformatics↗

bioRxiv2020

Oxidized LDL but not angiotensin II induces the interaction between LOX-1 and AT1 receptors

Oxidized low-density lipoprotein (Ox-LDL) can induce cardiac hypertrophy, but the mechanism is still unclear. Here we elucidate the role of angiotensin II (AngII) receptor (AT1-R) in Ox-LDL-induced cardiomycyte hypertrophy. Inhibition of Ox-LDL receptor LOX-1 and AT1-R rather than AngII abolished Ox-LDL-induced hypertrophic responses. Similar results were obtained from the heart of mice lacking endogenous Ang II and their cardiomyocytes. Ox-LDL but not AngII induced binding of LOX-1 to AT1-R, and the inhibition of LOX-1 or AT1-R rather than AngII abolished the association of these two receptors. Ox-LDL-induced ERKs phosphorylation in LOX-1 and AT1-R-overexpression cells and the binding of both receptors were suppressed by the mutants of LOX-1 (Lys266Ala/Lys267Ala) or AT1-R (Glu257Ala), however, the AT1-R mutant lacking Gq protein-coupling ability only abolished the ERKs phosphorylation. The phosphorylation of ERKs induced by Ox-LDL in LOX-1 and AT1-R-overexpression cells was abrogated by Gq protein inhibitor but not by Jak2, Rac1 and RhoA inhibitors. Therefore, the direct interaction between LOX-1 and AT1-R and the downstream Gq protein activation are important mechanisms for Ox-LDL-but not AngII-induced cardiomyocyte hypertrophy.

cell biology↗

bioRxiv2020

Rapid evolution of bacterial mutualism in the plant rhizosphere

Even though beneficial plant-microbe interactions are commonly observed in nature, direct evidence for the evolution of bacterial mutualism in the rhizosphere remains elusive. Here we use experimental evolution to causally show that initially plant-antagonistic Pseudomonas protegens bacterium evolves into mutualists in the rhizosphere of Arabidopsis thaliana within six plant growth cycles (6 months). This evolutionary transition was accompanied with increased mutualist fitness via two mechanisms: i) improved competitiveness for root exudates and ii) enhanced capacity for activating the root-specific transcription factor gene MYB72, which triggers the production of plant-secreted scopoletin antimicrobial for which the mutualists evolved relatively higher tolerance to. Genetically, mutualism was predominantly associated with different mutations in the GacS/GacA two-component regulator system, which conferred high fitness benefits only in the presence of plants. Together, our results show that bacteria can rapidly evolve along the parasitism-mutualism continuum in the plant rhizosphere at an agriculturally relevant evolutionary timescale.

microbiology↗

bioRxiv2020

Experimental evolution-driven identification of Arabidopsis rhizosphere competence genes in Pseudomonas protegens

Beneficial plant root-associated microorganisms carry out a range of functions that are essential for plant performance. Establishment of a bacterium on plant roots, however, requires overcoming several challenges, including competition with neighboring microorganisms and host immunity. Forward and reverse genetics has led to the identification of mechanisms that are used by beneficial microorganisms to overcome these challenges such as the production of iron-chelating compounds, the formation of strong biofilms, or the concealment of characteristic microbial molecular patterns that trigger the host immune system. However, how such mechanisms arose from an evolutionary perspective is much less understood. To study bacterial adaptation in the rhizosphere, we employed experimental evolution to track the physiological and genetic dynamics of root-dwelling Pseudomonas protegens in the Arabidopsis thaliana rhizosphere under axenic conditions. This simplified binary one plant-one bacterium system allows for the amplification of key adaptive mechanisms for bacterial rhizosphere colonization. We identified 35 mutations, including single-nucleotide polymorphisms, insertions, and deletions, distributed over 28 genes. We found that mutations in genes encoding global regulators, and in genes for siderophore production, cell surface decoration, attachment, and motility accumulated in parallel, underlining that bacterial adaptation to the rhizosphere follows multiple strategies. Notably, we observed that motility increased in parallel across multiple independent evolutionary lines. Altogether these results underscore the strength of experimental evolution to identify key genes, pathways, and processes for bacterial rhizosphere colonization, and a methodology for the development of elite beneficial microorganisms with enhanced root-colonizing capacities that can support sustainable agriculture in the future. ImportanceBeneficial root-associated microorganisms carry out many functions that are essential for plant performance. Establishment of a bacterium on plant roots, however, requires overcoming many challenges. Previously, diverse mechanisms that are used by beneficial microorganisms to overcome these challenges were identified. However, how such mechanisms have developed from an evolutionary perspective is much less understood. Here, we employed experimental evolution to track the evolutionary dynamics of a root-dwelling pseudomonad on the root of Arabidopsis. We find that mutations in global regulators, as well as in genes for siderophore production, cell surface decoration, attachment, and motility accumulate in parallel, underlining these strategies for bacterial adaptation to the rhizosphere. We identified 35 mutations distributed over 28 genes. Altogether our results demonstrate the power of experimental evolution to identify key pathways for rhizosphere colonization and a methodology for the development of elite beneficial microorganisms that can support sustainable agriculture.

microbiology↗

bioRxiv2020

A Novel SARS-CoV-2 Multitope Protein/Peptide Vaccine Candidate is Highly Immunogenic and Prevents Lung Infection in an Adeno Associated Virus Human Angiotensin-Converting Enzyme 2 (AAV hACE2) Mouse Model

A novel multitope protein-peptide vaccine against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and disease is described in this report. The initial development and characterization experiments are presented along with proof-of-concept studies for the vaccine candidate UB-612. UB-612 consists of eight components rationally designed for induction of potently neutralizing antibodies and broad T cell responses against SARS-CoV-2: the S1-RBD-sFc fusion protein, six synthetic peptides (one universal peptide and five SARS-CoV-2-derived peptides), a proprietary CpG TLR-9 agonist at low concentration as an excipient, and aluminum phosphate adjuvant. Through immunogenicity studies in Guinea pigs and rats, we optimized the design of protein/peptide immunogens and selected an adjuvant system, yielding a vaccine that provides excellent S1-RBD binding and high neutralizing antibody responses, robust cellular responses, and a Th1-oriented response at low doses. In challenge studies, UB- 612 vaccination reduced viral load and prevented development of disease in mouse and non-human primate challenge models. With a Phase 1 trial completed, a Phase 2 trial ongoing in Taiwan, and additional trials planned to support global authorizations, UB-612 is a highly promising and differentiated vaccine candidate for prevention of SARS-CoV-2 infection and COVID-19 disease. Author SummarySARS-CoV-2 virus, the causative agent of Coronavirus Disease 2019 (COVID-19), has spread globally since its origin in 2019, causing an unprecedented public health crisis that has resulted in greater than 4.7 million deaths worldwide. Many vaccines are under development to limit disease spread and reduce the number of cases, but additional candidates that promote a robust immune response are needed. Here, we describe a multitope protein-peptide vaccine platform that is unique among COVID-19 vaccines. The advantages of our approach are induction of both high levels of neutralizing antibodies as well as a Th/CTL response in the vaccinated host, which mimics the immune response that occurs after natural infection with SARS-CoV-2. We demonstrate that our vaccine is immunogenic and effective in preventing disease in several animal models, including AAV- hACE-2 transduced mice, and both rhesus and cynomolgus macaques. Importantly, no immunopathology was observed in the lungs of immunized animals, therefore showing that antibody-dependent enhancement (ADE) does not occur. Our study provides an additional, novel vaccine candidate for advancement in clinical trials to treat and prevent SARS-CoV-2 infection and COVID-19 disease.

immunology↗

bioRxiv2020

Intracellular localisation of Mycobacterium tuberculosis affects antibiotic efficacy

To be effective, chemotherapy against tuberculosis (TB) must kill the intracellular population of Mycobacterium tuberculosis (Mtb). However, how host cell environments affect antibiotic accumulation and efficacy remains elusive. Pyrazinamide (PZA) is a key antibiotic against TB, yet its behaviour is not fully understood. Here, by using correlative light, electron, and ion microscopy to image PZA at the subcellular level, we investigated how human macrophage environments affect PZA activity. We discovered that PZA accumulates heterogeneously between individual bacteria in multiple host cell environments. Crucially, Mtb phagosomal localisation and acidification increase PZA accumulation and efficacy. By imaging two antibiotics commonly used in combined TB therapy, we showed that bedaquiline (BDQ) significantly enhances PZA accumulation by a host cell mediated mechanism. Thus, intracellular localisation and specific microenvironments affect PZA accumulation and efficacy; explaining the potent in vivo efficacy compared to its modest in vitro activity and the critical contribution to TB combination chemotherapy.

microbiology↗

bioRxiv2020

Frameshift and frame-preserving mutations in zebrafish presenilin 2 affect different cellular functions in young adult brains

BackgroundMutations in PRESENILIN 2 (PSEN2) cause early disease onset familial Alzheimers disease (EOfAD) but their mode of action remains elusive. One consistent observation for all PRESENILIN gene mutations causing EOfAD is that a transcript is produced with a reading frame terminated by the normal stop codon - the "reading frame preservation rule". Mutations that do not obey this rule do not cause the disease. The reasons for this are debated. MethodsA frameshift mutation (psen2N140fs) and a reading frame-preserving mutation (psen2T141_L142delinsMISLISV) were previously isolated during genome editing directed at the N140 codon of zebrafish psen2 (equivalent to N141 of human PSEN2). We mated a pair of fish heterozygous for each mutation to generate a family of siblings including wild type and heterozygous mutant genotypes. Transcriptomes from young adult (6 months) brains of these genotypes were analysed. Bioinformatics techniques were used to predict cellular functions affected by heterozygosity for each mutation. ResultsThe reading frame preserving mutation uniquely caused subtle, but statistically significant, changes to expression of genes involved in oxidative phosphorylation, long term potentiation and the cell cycle. The frameshift mutation uniquely affected genes involved in Notch and MAPK signalling, extracellular matrix receptor interactions and focal adhesion. Both mutations affected ribosomal protein gene expression but in opposite directions. ConclusionA frameshift and frame-preserving mutation at the same position in zebrafish psen2 cause discrete effects. Changes in oxidative phosphorylation, long term potentiation and the cell cycle may promote EOfAD pathogenesis in humans.

bioinformatics↗

bioRxiv2020

Genome-wide screen of genomic imprinting in endosperm and population-level analysis reveal allelic variation for imprinting in flax

Genomic imprinting is an epigenetic phenomenon caused by the biased expression of maternally and paternally inherited alleles. In flowering plants, genomic imprinting predominantly occurs in triploid endosperm and plays a vital role in seed development. In this study, we identified 241 candidate imprinted genes including 143 maternally expressed imprinted genes (MEGs) and 98 paternally expressed imprinted genes (PEGs) in flax (Linum usitatissimum L.) endosperm using deep RNA sequencing. The conservation of imprinting in plants is very limited and imprinting clustering is not a general feature. MEGs tends to be endosperm expression specific, while PEGs are non-tissue specific. Imprinted SNPs differentiated 200 flax cultivars into oil flax, oil-fiber dual purpose flax (OF) and fiber flax subgroups, suggesting that genomic imprinting contributes to intraspecific variation in flax. The nucleotide diversity ({pi}) of imprinted genes in oil flax subgroup is significantly higher than that in fiber flax subgroup, indicating that some imprinted genes undergo positive selection during flax domestication from oil flax to fiber flax. Imprinted genes undergo positive selection is related to the functions. Eleven imprinted genes related to seed size and weight were identified using the candidate gene-based association study. Our study provides information for further exploring the function and genomic variation of imprinted genes in flax population.

plant biology↗

bioRxiv2020

Human fecal microbiota is associated with colorectal cancer

BackgroundColorectal cancer (CRC) is one of the most common cancers. In recent studies, the gut microbiota has been reported to be potentially involved in aggravating or favoring CRC development. However, little is known about the microbiota composition in CRC patients after treatment. In this study, we explored the fecal microbiota composition to obtain a periscopic view of gut microbial communities. We analyzed microbial 16S rRNA genes from 107 fecal samples of Chinese individuals from three groups, including 33 healthy individuals (Normal), 38 CRC patients (Fa), and 36 CRC post-surgery patients (Fb). ResultsSpecies richness and diversity were decreased in the Fa and Fb groups compared with that of the Normal group. Partial least squares discrimination analysis showed clustering of samples according to disease with an obvious separation between the Fa and Normal, and Fb and Normal groups, as well as a partial separation between the Fa and Fb groups. Based on linear discriminant analysis effect size analysis and a receiver operating characteristic model, Fusobacterium was suggested as a potential biomarker for CRC screening. Additionally, we found that surgery greatly reduced the bacterial diversity of microbiota in CRC patients. Some commensal beneficial bacteria of the intestinal canal, such as Faecalibacterium and Prevotella, were decreased, whereas the drug-resistant Enterococcus was visibly increased in CRC post-surgery group. Meanwhile, we observed a declining tendency of Fusobacterium in the majority of follow-up CRC patients who were still alive approximately 3 y after surgery. We also observed that beneficial bacteria dramatically decreased in CRC patients that recidivated or died after surgery. This revealed that important bacteria might be associated with prognosis. ConclusionsThe fecal bacterial diversity was diminished in CRC patients compared with that in healthy individuals. Enrichment and depletion of several bacterial strains associated with carcinomas and inflammation were detected in CRC samples. Fusobacterium might be a potential biomarker for early screening of CRC in Chinese or Asian populations. In summary, this study indicated that fecal microbiome-based approaches could be a feasible method for detecting CRC and monitoring prognosis post-surgery.

microbiology↗

bioRxiv2020

A versatile resource of 1500 diverse wild and cultivated soybean genomes for post-genomics research

With the advance of next-generation sequencing technologies, over 15 terabytes of raw soybean genome sequencing data were generated and made available in the public. To develop a consolidated, diverse, and user-friendly genomic resource to facilitate post-genomic research, we sequenced 91 highly diverse wild soybean genomes representing the entire US collection of wild soybean accessions to increase the genetic diversity of the sequenced genomes. Having integrated and analyzed the sequencing data with the public data, we identified and annotated 32 million single nucleotide polymorphisms (32mSNPs) with a resolution of 30 SNPs/kb and 12 non-synonymous SNPs/gene in 1,556 accessions (1.5K). Population structure analysis showed that the 1.5K accessions represent the genetic diversity of the 20,087 (20K) soybean accessions in the U.S. collection. Inclusion of wild soybean genomes significantly increased the genetic diversity and shorten linkage disequilibrium distance in the panel of soybean accessions. We identified a collection of paired accessions sharing the highest genomic identity between the 1.5K and 20K accessions as genomically "equivalent" accessions to maximize the use of the genome sequences. We demonstrated that the 32mSNPs in the 1.5K accessions can be effectively used for in-silico genotyping, discovering trait QTL, gene alleles/mutations, identifying germplasms containing beneficial allele and domestication selection of trait alleles. We made the 32mSNPs and 1.5K accessions with detailed annotation available at SoyBase and Ag Data Commons. The dataset could serve as a versatile resource to release the potential of the huge amount of genome sequencing data for a variety of postgenomic research.

plant biology↗

bioRxiv2020

CD127 imprints functional heterogeneity to diversify monocyte responses in human inflammatory diseases

Studies on human monocytes historically focused on characterization of bulk responses, whereas functional heterogeneity is largely unknown. Here, we identified an inducible population of CD127-expressing human monocytes under inflammatory conditions and named the subset M127. M127 is nearly absent in healthy individuals yet abundantly present in patients with infectious and inflammatory conditions such as COVID-19 and rheumatoid arthritis. Multiple genomic and functional approaches revealed unique gene signatures of M127 and unified anti-inflammatory properties imposed by the CD127-STAT5 axis. M127 expansion correlated with mild COVID-19 disease outcomes. Thereby, we phenotypically and molecularly characterized a human monocyte subset marked by CD127 that retained anti-inflammatory properties within the pro-inflammatory environments, uncovering remarkable functional diversity among monocytes and signifying M127 as a potential therapeutic target for human inflammatory disorders.

immunology↗

bioRxiv2020

Activating Immune Recognition in Pancreatic Ductal Adenocarcinoma Using Autophagy Inhibition, MEK blockade and CD40 Agonism

Pancreatic ductal adenocarcinoma (PDA) patients have not yet benefitted from the revolution in cancer immunotherapy due in large part to the dominantly immunosuppressive tumor microenvironment (TME). MEK inhibition combined with autophagy inhibition leads to transient tumor responses in some PDA patients. We find that co-inhibition of MEK (using cobimetinib, COBI) and autophagy (using mefloquine, MFQ), but not either treatment alone, activates the Type I Interferon/STING pathway in tumor cells which in turn reprogram tumor associated macrophages (TAMs) in paracrine to foster an immunogenic switch. This effect is augmented by a CD40 agonist (aCD40). Triple therapy (COBI+MFQ+aCD40) achieved cytotoxic T cell activation in an immunologically "cold" mouse PDA model, leading to enhanced anti-tumor immunity. Collectively, MEK and autophagy co-inhibition coupled with CD40 agonism invokes immuno-reprograming and is an attractive therapeutic approach for PDA immunotherapy development.

cancer biology↗

bioRxiv2020

Structural basis for repurpose and design of nucleoside drugs for treating COVID-19

SARS-CoV-2 has caused a global pandemic of COVID-19 that urgently needs an effective treatment. Nucleoside analog drugs including favipiravir have been repurposed for COVID-19 despite of unclear mechanism of their inhibition of the viral RNA polymerase (RdRp). Here we report the cryo-EM structures of the viral RdRp in complex with favipiravir and two other nucleoside inhibitor drugs ribavirin and penciclovir. Ribavirin and the ribosylated form of favipiravir share a similar ribose scaffold that is distinct from penciclovir. However, the structures reveal that all three inhibitors are covalently linked to the primer strand in a monophosphate form despite the different chemical scaffolds between favipiravir and penciclovir. Surprisingly, the base moieties of these inhibitors can form mismatched pairs with the template strand. Moreover, in view of the clinical disadvantages of remdesivir mainly associated with its prodrug form, we designed several orally-available remdesivir parent nucleoside derivatives, including VV16 that showed 5-fold more potent than remdesivir in inhibition of viral replication. Together, these results demonstrate an unexpected promiscuity of the viral RNA polymerase and provide a basis for repurpose and design of nucleotide analog drugs for COVID-19. One Sentence SummaryCryo-EM structures of the RNA polymerase of SARS-CoV-2 reveals the basis for repurposing of old nucleotide drugs to treat COVID-19.

biophysics↗

bioRxiv2020

Genetic determinants of COVID-19 drug efficacy revealed by genome-wide CRISPR screens

Immunomodulatory agents dexamethasone and colchicine, antiviral drugs remdesivir, favipiravir and ribavirin, as well as antimalarial drugs chloroquine phosphate and hydroxychloroquine are currently used in the combat against COVID-191-16. However, whether some of these drugs have clinical efficacy for COVID-19 is under debate. Moreover, these drugs are applied in COVID-19 patients with little knowledge of genetic biomarkers, which will hurt patient outcome. To answer these questions, we designed a screen approach that could employ genome-wide sgRNA libraries to systematically uncover genes crucial for these drugs action. Here we present our findings, including genes crucial for the import, export, metabolic activation and inactivation of remdesivir, as well as genes that regulate colchicine and dexamethasones immunosuppressive effects. Our findings provide preliminary information for developing urgently needed genetic biomarkers for these drugs. Such biomarkers will help better interpret COVID-19 clinical trial data and point to how to stratify COVID-19 patients for proper treatment with these drugs.

pharmacology and toxicology↗

bioRxiv2020

Deciphering the mechanism underlying circRNA-mediated immune responses of western honeybees to Nosema ceranae infection

Nosema ceranae is a widespread fungal parasite for adult honeybees, severely damaging bee health and sustainable development of apiculture. Circular RNAs (circRNAs) are a class of newly discovered noncoding RNAs (ncRNAs) that regulate a number of biological processes such as immune defense and development. In this current work, based on previously obtained whole transcriptome data, 8 199 and 8 711 circRNAs were predicted from the midguts of Apis mellifera ligustica workers at 7 days (AmT1) and 10 days (AmT2) post inoculation (dpi) with N. ceranae using bioinformatics. Additionally, in combination with transcriptome data from uninfected midguts (AmCK1 and AmCK2) (Xiong et al., 2018), 4 464 circRNAs were found to be shared by the aforementioned four groups, whereas the numbers of specifically transcribed circRNAs in each group were 1 389, 1 696, 1 019 and 1 871, respectively. Furthermore, 10 226 circRNAs were homologous to Apis cerana cerana circRNAs, while 20 circRNAs had homology with Homo sapiens circRNAs; in addition, 16 circRNAs were highly conserved in these three species. Differential expression analysis showed that 168 (306) differentially expressed circRNAs (DEcircRNAs) were identified in AmCK1 vs AmT1 (AmCK2 vs AmT2) comparison group, including 61 (143) upregulated circRNAs and 107 (163) downregulated circRNAs. Moreover, RT-qPCR results showed that the expression trend of eight DEcircRNAs was consistent with that of the transcriptome dataset. Based on GO database annotation, we observed that source genes of DEcircRNAs in AmCK1 vs AmT1 (AmCK2 vs AmT2) were engaged in 27 (35) functional terms, including two (two) cell renewal-associated terms, seven (seven) cell structure-associated terms, and one (one) immunity-associated terms. Additionally, DEcircRNA source genes in AmCK1 vs AmT1 were involved in two cell renewal-related pathways, Hippo and Wnt signaling pathways, and three carbohydrate metabolism-related pathways, galactose metabolism, starch and sucrose metabolism, fructose and mannose metabolism, only one energy metabolism-related pathway (oxidative phosphorylation pathway), three cellular immune-related pathways, endocytosis, phagosome, and lysosome, and a humoral immune-related pathway (FoxO signaling pathway). In AmCK2 vs AmT2 comparison group, more source genes of DEcircRNAs were associated with the abovementioned pathways relative to cell renewal, carbohydrate metabolism, and cellular and humoral immune pathways. In addition, 122 (234) DEcircRNAs in the host midgut at 7 dpi (10 dpi) with N. ceranae targeted 82 (106) miRNAs. Furthermore, 75 (103) miRNAs targeted by 86 (178) DEcircRNAs in AmCK1 vs AmT1 (AmCK2 vs AmT2) further bound to 215 (305) mRNAs. These targets could be annotated as an array of functional terms and pathways related to cellular renewal, cellular structure, carbohydrate and energy metabolism, and cellular and humoral immunity. In a word, we for the first time explored immune responses mediated by DEcircRNAs in the midguts of A. m. ligustica workers to N. ceranae infection. Our data provide a foundation for clarifying the molecular mechanism underlying immune response of western honeybee to N. ceranae invasion, but also a new insight into further understanding the host-pathogen interaction during bee microsporidiosis.

genomics↗

bioRxiv2020

Duple extinguishment of COVID-19: single compound synergized inhibition of SARS-CoV-2 replication and direct suppression of inflammatory cytokines in vitro/vivo

We firstly disclose single compound yields better therapeutic outcome than Remdesivir in COVID-19 hamster treatments as it is armed with direct inhibition viral replication and intrinsic suppression inflammatory cytokines expression. Crystal data reveals that Au (I), released from Au22Glutathione18 (GA), covalently binds thiolate of Cys145 of SARS-CoV-2 Mpro. GA directly decreases SARS-CoV-2 viral replication (EC50: ~0.24 M) and intrinsically down-regulates NF{kappa}B pathway therefore significantly inhibiting expression of inflammatory cytokines in cells. The lung viral load and inflammatory cytokines in GA-treated COVID-19 transgenic mice are found to be significantly lower than that of control mice. When COVID-19 golden hamsters are treated by GA, the lung inflammatory cytokines levels are significantly lower than that of Remdesivir while their lung viral load are decreased to same level. The pathological results show that GA treatment significantly reduce lung inflammatory injuries when compared to that of Remdesivir-treated COVID-19 golden hamsters. One Sentence SummaryWe found that gold cluster molecule directly inhibits SARS-CoV-2 replication and intrinsically suppresses inflammatory cytokines expression in COVID-19 transgenic mouse and golden hamster model, gold cluster providing a better lung injury protection than Remdesivir in COVID-19 golden hamsters via intranasally dropping administration.

microbiology↗