Biology subjects

Zhao, L.

Publications and source records attributed to Zhao, L..

At least 325 records · Page 18Linked to original sources

bioRxiv2020

Transcription factors drive opposite relationships between gene age and tissue specificity in male and female Drosophila gonads

Evolutionarily young genes are usually preferentially expressed in the testis across species. While it is known that older genes are generally more broadly expressed than younger genes, the properties that shaped this pattern are unknown. Older genes may gain expression across other tissues uniformly, or faster in certain tissues than others. Using Drosophila gene expression data, we confirmed previous findings that younger genes are disproportionately testis-biased and older genes are disproportionately ovary-biased. We found that the relationship between gene age and expression is stronger in the ovary than any other tissue, and weakest in testis. We performed ATAC-seq on Drosophila testis and found that while genes of all ages are more likely to have open promoter chromatin in testis than in ovary, promoter chromatin alone does not explain the ovary-bias of older genes. Instead, we found that upstream transcription factor (TF) expression is highly predictive of gene expression in ovary, but not in testis. In ovary, TF expression is more predictive of gene expression than open promoter chromatin, whereas testis gene expression is similarly influenced by both TF expression and open promoter chromatin. We propose that the testis is uniquely able to expresses younger genes controlled by relatively few TFs, while older genes with more TF partners are broadly expressed with peak expression most likely in ovary. The testis allows widespread baseline expression that is relatively unresponsive to regulatory changes, whereas the ovary transcriptome is more responsive to trans-regulation and has a higher ceiling for gene expression.

evolutionary biology↗

bioRxiv2020

Effect of the BMPR-II-SMAD3/MRTF complex on proliferation and migration of ASMCs and the mechanism in asthma.

Phenotype transformation of airway smooth muscle (ASM) is the key feature of airway remodelling in asthma. A variety of smooth muscle-specific genes and proteins, including SMAD3, BMPR-II, and MRTF, are involved in airway remodelling in asthma. Bone morphogenetic protein (BMP) signalling plays an important role in the physiological and pathological processes of asthma. As a receptor of BMP signalling, BMPR-II has important roles in variety of cellular processes. However, the understanding of the roles and underlying mechanism of BMPR-II in airway smooth muscle cells (ASMCs) in asthma remains incomplete. First, we observed significant increases in BMPR-II, SMAD3 and MRTF in asthmatic ASMCs at both the mRNA and protein levels. Second, we observed that silencing of siBMPR-II and siMRTF inhibits proliferation, migratory capacity and intracellular Ca2+ concentration in ASMCs. Furthermore, our results revealed these three factors, BMPR-II, SMAD3 and MRTF, form a complex that affects the bioactivities of ASMCs. Taken together, this study indicates that the BMPR-II-SMAD3/MRTF signalling pathway is involved in the process of ASM remodelling, providing novel avenues for the identification of new therapeutic modalities.

cell biology↗

bioRxiv2020

Distinct hydrogenotrophic bacteria are stimulated by elevated H2 levels in upland and wetland soils

BackgroundMolecular hydrogen (H2) is a major energy source supporting bacterial growth and persistence in soil ecosystems. While recent studies have uncovered mediators of atmospheric H2 consumption, far less is understood about how soil microbial communities respond to elevated H2 levels produced through natural or anthropogenic processes. Here we performed microcosm experiments to resolve how microbial community composition, capabilities, and activities change in upland (meadow, fluvo-aquic soil) and wetland (rice paddy, anthrosols soil) soils following H2 supplementation (at mixing doses from 0.5 to 50,000 ppmv). ResultsGenome-resolved metagenomic profiling revealed that these soils harbored diverse bacteria capable of using H2 as an electron donor for aerobic respiration (46 of the 196 MAGs from eight phyla) and carbon fixation (15 MAGs from three phyla). H2 stimulated the growth of several of these putative hydrogenotrophs in a dose-dependent manner, though the lineages stimulated differed between the soils; whereas actinobacterial lineages encoding group 2a [NiFe]-hydrogenases grew most in the upland soils (i.e. Mycobacteriaceae, Pseudonocardiaceae), proteobacterial lineages harboring group 1d [NiFe]-hydrogenases were most enriched in wetland soils (i.e. Burkholderiaceae). Hydrogen supplementation also influenced the abundance of various other genes associated with biogeochemical cycling and bioremediation pathways to varying extents between soils. Reflecting this, we observed an enrichment of a hydrogenotrophic Noviherbaspirillum MAG capable of biphenyl hydroxylation in the wetland soils and verified that H2 supplementation enhanced polychlorinated biphenyl (PCB) degradation in these soils, but not the upland soils. ConclusionsOur findings suggest that soils harbour different hydrogenotrophic bacteria that rapidly grow following H2 exposure. In turn, this adds to growing evidence of a large and robust soil H2 sink capable of counteracting growing anthropogenic emissions.

bioinformatics↗

bioRxiv2020

Sex-specific Alterations in Hepatic Cholesterol Metabolism in Young Uteroplacental Insufficiency-induced Low Birth Weight Adult Guinea Pig Offspring

BackgroundIntrauterine growth restriction (IUGR) and low birth weight (LBW) have been widely reported as an independent risk factor for hypercholesterolemia and increased hepatic cholesterol underlying liver dysfunction in adulthood. However, the specific impact of uteroplacental insufficiency (UPI), a leading cause of LBW in developed world, on hepatic cholesterol metabolism in later life, is ill defined and is clinically relevant in understanding later life liver metabolic health trajectories. MethodsHepatic cholesterol metabolism pathways were studied in uterine artery ablation-induced LBW and normal birth weight (NBW) male and female guinea pig offspring at postnatal day 150. ResultsHepatic free and total cholesterol were increased in LBW versus NBW males. Transcriptome analysis of LBW versus NBW livers revealed that "Cholesterol metabolism" was an enriched pathway in LBW males but not females. Microsomal triglyceride transfer protein and cytochrome P450 7A1 protein, involved in hepatic cholesterol efflux and catabolism, respectively, and catalase activity were decreased in LBW male livers. Superoxide dismutase activity was reduced in LBW males but increased in LBW females. ConclusionsUPI environment is associated with a later life programed hepatic cholesterol accumulation via impaired cholesterol elimination, in a sex-specific manner. These programmed alterations could underlie later life cholesterol-induced hepatic lipotoxicity in LBW male offspring. Impact StatementO_LILow birth weight (LBW) is a risk factor for adult hypercholesterolemia and increased hepatic cholesterol. C_LIO_LIUteroplacental insufficiency (UPI) resulting in LBW increased hepatic cholesterol content, altered hepatic expression of cholesterol metabolism-related genes in young adult guinea pigs. C_LIO_LIUPI-induced LBW was also associated with markers of a compromised hepatic cholesterol elimination process and failing antioxidant system in young adult guinea pigs. C_LIO_LIThese changes, at the current age studied, were sex-specific, only being observed in LBW males and not LBW females. C_LIO_LIThese programmed alterations could lead to further hepatic damage and greater predisposition to liver diseases in UPI-induced LBW male offspring as they age. C_LI

physiology↗

bioRxiv2020

Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2

The ongoing SARS-CoV-2 pandemic has brought an urgent need for animal models to study the pathogenicity of the virus. Herein, we generated and characterized a novel mouse-adapted SARS-CoV-2 strain, named MASCp36, that causes severe acute respiratory symptoms and mortality in standard laboratory mice. Particularly, this model exhibits age and gender related skewed distribution of mortality akin to severe COVID-19, and the 50% lethal dose (LD50) of MASCp36 was 58 PFU in 9-month-old, male BALB/c mice. Deep sequencing identified three amino acid substitutions, N501Y, Q493H, and K417N, subsequently emerged at the receptor binding domain (RBD) of MASCp36, during in vivo passaging. All three mutations in RBD significantly enhanced the binding affinity to its endogenous receptor, mouse ACE2 (mACE2). Cryo-electron microscopy (cryo-EM) analysis of human ACE2 (hACE2) or mACE2 in complex with the RBD of MASCp36 at 3.1 to 3.7 angstrom resolution elucidates molecular basis for the receptor-binding switch driven by specific amino acid substitutions. Interestingly, N501Y and Q493H enhanced the binding affinity to human ACE2 (hACE2); while triple mutations N501Y/Q493H/K417N decreased affinity to hACE2, thus led to the reduced infectivity of MASCp36 to human cells. Our study not only provides a robust platform for studying the pathogenesis of severe COVID-19 and rapid evaluation of coutermeasures against SARS-CoV-2, but also unveils the molecular mechanism for the rapid adaption and evolution of SARS-CoV-2 in human and animals. One sentence summaryA mouse adapted SARS-CoV-2 strain that harbored specific amino acid substitutions in the RBD of S protein showed 100% mortality in aged, male BALB/c mice.

microbiology↗

bioRxiv2020

Behavioral and genomic sensory adaptations underlying the pest activity of Drosophila suzukii

Studying how novel phenotypes originate and evolve is fundamental to the field of evolutionary biology as it allows us to understand how organismal diversity is generated and maintained. However, determining the basis of novel phenotypes is challenging as it involves orchestrated changes at multiple biological levels. Here, we aim to overcome this challenge by using a comparative species framework combining behavioral, gene expression, and genomic analyses to understand the evolutionary novel egg-laying substrate-choice behavior of the invasive pest species Drosophila suzukii. First, we used egg-laying behavioral assays to understand the evolution of ripe fruit oviposition preference in D. suzukii as compared to closely related species D. subpulchrella and D. biarmipes, as well as D. melanogaster. We show that D. subpulchrella and D. biarmipes lay eggs on both ripe and rotten fruits, suggesting that the transition to ripe fruit preference was gradual. Secondly, using two-choice oviposition assays, we studied how D. suzukii, D. subpulchrella, D. biarmipes and D. melanogaster differentially process key sensory cues distinguishing ripe from rotten fruit during egg-laying. We found that D. suzukiis preference for ripe fruit is in part mediated through a species-specific preference for stiff substrates. Lastly, we sequenced and annotated a high-quality genome for D. subpulchrella. Using comparative genomic approaches, we identified candidate genes involved in D. suzukiis ability to seek out and target ripe fruits. Our results provide detail to the stepwise evolution of pest activity in D. suzukii, indicating important cues used by this species when finding a host, and the molecular mechanisms potentially underlying their adaptation to a new ecological niche.

evolutionary biology↗

bioRxiv2020

Rapid Development of Neutralizing and Diagnostic SARS-COV-2 Mouse Monoclonal Antibodies

The need for high-affinity, SARS-CoV-2-specific monoclonal antibodies (mAbs) is critical in the face of the global COVID-19 pandemic, as such reagents can have important diagnostic, research, and therapeutic applications. Of greatest interest is the ~300 amino acid receptor binding domain (RBD) within the S1 subunit of the spike protein because of its key interaction with the human angiotensin converting enzyme 2 (hACE2) receptor present on many cell types, especially lung epithelial cells. We report here the development and functional characterization of 29 nanomolar-affinity mouse SARS-CoV-2 mAbs created by an accelerated immunization and hybridoma screening process. Differing functions, including binding of diverse protein epitopes, viral neutralization, impact on RBD-hACE2 binding, and immunohistochemical staining of infected lung tissue, were correlated with variable gene usage and sequence.

immunology↗

bioRxiv2020

Tropomyosin in mugwort cross-reacts to house dust mite, eliciting non-Th2 response in allergic rhinitis patients sensitized to house dust mite

BackgroundMugwort and house dust mite (HDM) are two of the most common inhalant allergens in Asia; however, whether or not mugwort affects polysensitized HDM+ allergic rhinitis (AR) patients has not been elucidated. MethodsOverall, 15884 AR outpatients were assessed for clinical status. Amino acid sequences of mugwort were determined by mass spectrometry. Afterward, cross-reactivity between mugwort tropomyosin and Dermatophagoides pteronyssinus 10 (Der p10) was analysed by ELISA inhibition and basophils activation experiments. To compare immunologic responses eliciting by two different tropomyosins, peripheral blood mononuclear cells (PBMCs) of HDM-monosensitized patients were stimulated by mugwort, HDM, Der p10 and synthetic peptides representing mugwort tropomyosin respectively. ResultsPolysensitized HDM+AR patients were mainly sensitized to cat and mugwort, and the positive rate of monosensitized HDM+AR out-clinic patients was increased during the mugwort pollen season. Mugwort tropomyosin protein had similar structural domains to HDM tropomyosin, Der p10. ELISA inhibition experiment showed synthetic mugwort tropomyosin peptide inhibited IgE binding to Der p10; mugwort tropomyosin peptide activated basophils which were primed by HDM-specific IgE. Unlike HDM and Derp 10, mugwort and mugwort tropomyosin mainly induced IFN-{gamma} and IL-17, release in PBMCs of monosensitized HDM+AR patients, but not IL-5. ConclusionsPan-allergen tropomyosin is a major protein accounting for the cross-reactivity between mugwort and HDM, which reminds HDM+ patients to reduce mugwort exposure in mugwort pollen season in virtue of the tropomyosin induced mild inflammation.

immunology↗

bioRxiv2020

Long-term survival of salmon-attached SARS-CoV-2 at 4 degree as a potential source of transmission in seafood markets

Several outbreaks of COVID-19 were associated with seafood markets, raising concerns that fish-attached SARS-CoV-2 may exhibit prolonged survival in low-temperature environments. Here we showed that salmon-attached SARS-CoV-2 at 4{degrees}C could remain infectious for more than one week, suggesting that fish-attached SARS-CoV-2 may be a source of transmission.

microbiology↗

bioRxiv2020

Low XIST expression in Sertoli cells of Klinefelter syndrome patients caused the high susceptibility of these cells to an extra X chromosome

Klinefelter syndrome (KS) is the most common genetic cause of human male infertility. Patients suffer from heterogeneous testicular atrophy with loss of both germ cells and Sertoli cells. However, the mechanism by which the extra X chromosome causes failure of spermatogenesis remains poorly understood. Here, we profiled testicular single-cell transcriptomes from three KS patients and compared the results with those of healthy donors. Among different somatic cells, Sertoli cells showed the greatest changes in KS patients. Further analysis showed that XIST, a key long intergenic non-coding RNA that inactivates one X chromosome in female mammals, was widely expressed in somatic cells, except for Sertoli cells, leading to an increase in X-inactivation genes in these cells, which may cause Sertoli cells death and disruption of the spermatogenic microenvironment. Our study proposed a new mechanism to explain the unique pathological manifestations of KS in the testes and provided a theoretical basis for subsequent research and related treatment.

genomics↗

bioRxiv2020

The immunodominant and neutralization linear epitopes for SARS-CoV-2

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) becomes a tremendous threat to global health. Although vaccines against the virus are under development, the antigen epitopes on the virus and their immunogenicity are poorly understood. Here, we simulated the three-dimensional structures of SARS-CoV-2 proteins with high performance computer, predicted the B cell epitopes on spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins of SARS-CoV-2 using structure-based approaches, and then validated the epitope immunogenicity by immunizing mice. Almost all 33 predicted epitopes effectively induced antibody production, six of which were immunodominant epitopes in patients identified via the binding of epitopes with the sera from domestic and imported COVID-19 patients, and 23 were conserved within SARS-CoV-2, SARS-CoV and bat coronavirus RaTG13. We also found that the immunodominant epitopes of domestic SARS-CoV-2 were different from that of the imported, which may be caused by the mutations on S (G614D) and N proteins. Importantly, we validated that eight epitopes on S protein elicited neutralizing antibodies that blocked the cell entry of both D614 and G614 pseudo-virus of SARS-CoV-2, three and nine epitopes induced D614 or G614 neutralizing antibodies, respectively. Our present study shed light on the immunodominance, neutralization, and conserved epitopes on SARS-CoV-2 which are potently used for the diagnosis, virus classification and the vaccine design tackling inefficiency, virus mutation and different species of coronaviruses.

immunology↗

bioRxiv2020

High expression of angiotensin-converting enzyme-2 (ACE2) on tissue macrophages that may be targeted by virus SARS-CoV-2 in COVID-19 patients

Angiotensin-converting enzyme-2 (ACE2) has been recognized as the binding receptor for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that infects host cells, causing the development of the new coronavirus infectious disease (COVID-19). To better understand the pathogenesis of COVID-19 and build up the host anti-viral immunity, we examined the levels of ACE2 expression on different types of immune cells including tissue macrophages. Flow cytometry demonstrated that there was little to no expression of ACE2 on most of the human peripheral blood-derived immune cells including CD4+ T, CD8+ T, activated CD4+ T, activated CD8+ T, CD4+CD25+CD127low/- regulatory T cells (Tregs), Th17 cells, NKT cells, B cells, NK cells, monocytes, dendritic cells (DCs), and granulocytes. Additionally, there was no ACE2 expression (< 1%) found on platelets. Compared with interleukin-4-treated type 2 macrophages (M2), the ACE2 expression was markedly increased on the activated type 1 macrophages (M1) after the stimulation with lipopolysaccharide (LPS). Immunohistochemistry demonstrated that high expressions of ACE2 were colocalized with tissue macrophages, such as alveolar macrophages found within the lungs and Kupffer cells within livers of mice. Flow cytometry confirmed the very low level of ACE2 expression on human primary pulmonary alveolar epithelial cells. These data indicate that alveolar macrophages, as the frontline immune cells, may be directly targeted by the SARS-CoV-2 infection and therefore need to be considered for the prevention and treatment of COVID-19.

immunology↗

bioRxiv2020

Molecular and clinicopathological characterization of a prognostic immune gene signature associated with MGMT methylation in glioblastoma

BackgroundO6-methylguanine-DNA methyltransferase (MGMT) methylation status affects tumor chemo-resistance and the prognosis of glioblastoma (GBM) patients. We aimed to investigate the role of MGMT methylation in the regulation of GBM immunophenotype and discover an effective biomarker to improve prognosis prediction of GBM patients. MethodsA total of 769 GBM patients with clinical information from five independent cohorts were enrolled in the present study. Samples from the Cancer Genome Atlas (TCGA) dataset were used as the training set, whereas transcriptome data from the Chinese Glioma Genome Atlas (CGGA) RNA-seq, CGGA microarray, GSE16011, and the Repository for Molecular Brain Neoplasia (REMBRANDT) cohort were used for validation. A series of bioinformatics approaches were carried out to construct a prognostic signature based on immune-related genes, which were tightly related with the MGMT methylation status. The influence of the signature on immunosuppression and remodeling of the tumor microenvironment were comprehensively investigated. Then, the utility of this immune gene signature was analyzed by the development and evaluation of a nomogram. ResultsWe found that MGMT unmethylation was closely associated with immune-related biological processes in GBM. Sixty-five immune genes were more highly expressed in the MGMT unmethylated than the MGMT methylated group. An immune gene-based risk model was further established to divide patients into high and low-risk groups, and the prognostic value of this signature was validated in several GBM cohorts. Functional analyses manifested a universal up-regulation of immune-related pathways in the high-risk group as compared to the low-risk group. Furthermore, the risk score was highly correlated to the immune cell infiltration, immunosuppression, inflammatory activities, as well as the expression levels of immune checkpoints. Finally, a nomogram was developed for clinical application. ConclusionsMGMT methylation is strongly related to the immune responses in GBM. The immune gene-based signature we identified may have potential implications in predicting the prognosis of GBM patients and mechanisms underlying the role of MGMT methylation.

cancer biology↗

bioRxiv2020

Unravel the Mystery of NIC1-locus on Nicotine Biosynthesis Regulation in Tobacco

ABSTRACTBackground Nicotine biosynthesis is mainly regulated by jasmonate (JA) signaling cascade in Nicotiana tabacum. As an allotetraploid species, the regulation of nicotine biosynthesis has been genetically verified via two unlinked NIC loci (named as NIC1 and NIC2) which are possibly originated from its two ancestral diploids. Previously, a N. tomentosiformis originated ethylene response factor (ERF) gene cluster was identified as the NIC2-locus which has been demonstrated positively regulates nicotine accumulation in N. tabacum.Results Here, we describe the genetic mapping of NIC1-locus, the major nicotine regulatory locus, by using a NIC1-locus segregating population through bulked segregant analysis. We identified two linkage marker TM23004 and TM22038 were delimited the NIC1-locus within a ~34.3-Mb genomic region at pseudochromosome 07 of tobacco genome. Genomic scan within this region revealed a NIC2-like locus ERF gene cluster exist in. To verify this ERF gene cluster is the genetically called “NIC1-locus”, different functional experiments based on most of the ERFs in regulating nicotine biosynthesis and their influences on alkaloid accumulations have been carried out. Collinearity analysis showed that NIC1-locus ERF genes are originated from N. sylvestris and exclusively expressed in root tissues. In addition, transcriptomic results indicate that NIC1-locus ERF genes are coexpressed with the NIC2-locus ERF genes and other nicotine biosynthetic genes and regulators after JA induction. Furthermore, the suppressed expression of four ERFs of the NIC1-locus genes corresponding with decreased NtPMT and NtQPT expression in NtMYC2-RNAi lines indicates the selected NIC1-locus ERFs function in downstream of NtMYC2 in the JA signaling cascades. In the meanwhile, the alkaloid levels are also determined by the amplitude of the four ERF gene expressions in both wild type and LA mutant. Additionally, in vitro binding assays, transient activation assays, and ectopic expression in transgenic plants demonstrate that these ERF genes are able to bind the GCC-box elements residing in the step-limiting gene promoters (such as NtPMT2, NtQPT2) and functional redundant but quantitatively transactivate nicotine biosynthetic gene expression. For nic1-locus mutation, two different sizes of deletions (nic1-S and nic1-B) were identified which occurred at the surrounding regions of the NIC1-locus gene cluster, which might disrupt, to some extent, chromosomal microenvironment and change gene expression around the deletion regions (including NIC1-locus ERFs), resulting in the decreased expression levels of NIC1-locus ERFs (such as NtERF199) and reduced alkaloid accumulation in the nic1-locus mutant.Conclusions Our findings not only provide insight in to the mechanism of the NIC1-locus ERFs in the regulatory network of nicotine biosynthesis, but also unraveled the theoretical basis of the nic1-locus mutation in low nicotine mutant. These functional verified NIC1-locus ERF genes can be further used as potential target(s) for ethyl methanesulfonate-based mutagenesis to manipulate nicotine level in tobacco variety in tobacco breeding program.Competing Interest StatementThe authors have declared no competing interest.AbbreviationsA622a PIP family oxidoredutase for nicotine precursors condensationODCornithine decarboxylaseADCarginine decarboxylasePMTputrescine N-methyltransferaseMPON-methylputrescine oxidaseAOaspartate oxidaseQSquinolinic acid synthaseQPTqunolinic acid phosphoribosyl transferaseSPDSspermidine synthaseSAMSS-adenosylmethionine synthaseSAMDCS-adenosylmethione decarboxylasePCRPolymerase chain reactionRNA-seqRNA SequencingRPKMReads Per Kilobase per Million mapped readsSSRsimple sequence repeatqRT-PCRQuantitative real-time PCRCRchromosome rearrangementCNVcopy number variantView Full Text

plant biology↗

bioRxiv2020

Phosphoproteomics Reveals AMPK Substrate Network in Response to DNA Damage and Histone Acetylation

AMPK is a conservative energy sensor that plays roles in diverse biologic processes via direct phosphorylation on various substrates. Emerging studies have demonstrated the regulatory roles of AMPK in DNA repair, but the underlying mechanisms remain to be fully understood. Herein, using mass spectrometry-based proteomic technologies, we systematically investigate the regulatory network of AMPK in DNA damage response. Our system-wide phosphoproteome study uncovers a variety of newly-identified potential substrates involved in diverse biologic processes, whereas our system-wide histone modification analysis reveals a linkage between AMPK and histone acetylation. Together with these findings, we discover that AMPK promotes apoptosis by phosphorylating ASPP2 in irradiation-dependent way and regulates histone acetylation by phosphorylating HDAC9 in irradiation-independent way. Besides, we reveal that disturbing the histone acetylation by the bromodomain BRD4 inhibitor JQ-1 enhanced the sensitivity of AMPK-deficient cells to irradiation. Therefore, our studies provided a source to study the phosphorylation and histone acetylation underlying the regulatory network of AMPK, which could be beneficial to understand the exact role of AMPK in DNA damage response.Competing Interest StatementThe authors have declared no competing interest.View Full Text

cell biology↗

bioRxiv2020

In Vitro efficacy comparison of linezolid, tedizolid, sutezolid and delpazolid against rapid growing Mycobacteria isolated in Beijing, China

The natural resistance of rapid growth Mycobacterium (RGM) against multiple antibiotics renders the treatment of caused infections less successful and time consuming. Therefore, new effective agents are urgently needed. The aim of this study was to evaluate the in vitro susceptibility of 115 isolates, constituting different RGM species, against four oxazolidinones i.e. delpazolid, sutezolid, tedizolid and linezolid. Additionally, 32 reference strains of different RGM species were also tested. The four oxazolidinones exhibited potent in vitro activity against the recruited RGM reference strains, 24 out of 32 RGM species had MICs [≤] 8 g/mL against all four oxazolidinones whereas tedizolid and delpazolid generally presented lower MICs than linezolid or sutezolid. Tedizolid showed the strongest activity against clinical isolates of M. abscessus with MIC50=1g/mL and MIC90=2g/mL. MIC values for tedizolid were usually 4- to 8-fold less than the MICs of linezolid for M. abscessus subsp. abscessus. The MIC distributions of sutezolid and linezolid were similar, while delpazolid showed 2-fold lower MIC as compared with linezolid. Linezolid was not active against most of the tested M. fortuitum isolates, 22 out of the 25 M. fortuitum were resistant against linezolid. However, delpazolid exhibited better antimicrobial activity against these isolates with 4-fold lower MIC values, in contrast with linezolid. In addition, the protein alignment of RplC and RplD and structure based analysis showed that there may be no correlation between oxazolidinones resistance and mutations in rplC, rplD and 23 srRNAgenes in tested RGM. This study showed tedizolid harbors the strongest inhibitory activity against M. abscessus in vitro, while delpazolid presented the best activity against M. fortuitum, which provided important insights on the potential clinical application of oxazolidinones to treat RGM infections.

microbiology↗

bioRxiv2020

Altered N-glycan composition impacts flagella mediated adhesion in Chlamydomonas reinhardtii

For the unicellular alga Chlamydomonas reinhardtii, the presence of N-glycosylated proteins on the surface of two flagella is crucial for both cell-cell interaction during mating and flagellar surface adhesion. It is unknown whether the composition of N-glycans attached to respective proteins is important for these processes. To this end, we examined several C. reinhardtii insertional mutants and a CRIPSR/Cas9 knockout mutant of xylosyltransferase 1A, all possessing altered N-glycan compositions. Taking advantage of atomic force microscopy and micropipette force measurements, our data revealed that reduction in N-glycan complexity impedes the adhesion force required for binding the flagella to surfaces. In addition, polystyrene bead binding and transport is impaired. Notably, assembly, Intraflagellar Transport and FMG-1B transport into flagella are not affected by altered N-glycosylation. Thus, we conclude that proper N-glycosylation of flagellar proteins is crucial for adhering C. reinhardtii cells onto surfaces, indicating that N-glycans mediate surface adhesion via direct surface contact.

plant biology↗

bioRxiv2020

Molecular and clinical characterization of 5mC regulators in glioma: results of a multicenter study

DNA methylation has been widely reported to associate with the progression of glioma. DNA methylation at the 5 position of cytosine (5-methylcytosine, 5mC), which is regulated by 5mC regulators ("writers", "erasers" and "readers"), is the most critical modification pattern. However, a systematic study on the role of these regulators in glioma is still lacking. In this study, we collected gene expression profiles and corresponding clinical information of gliomas from three independent public datasets. Gene expression of 21 5mC regulators was analyzed and linked to clinicopathological features. A novel molecular classification of glioma was developed using consensus non-negative matrix factorization (CNMF) algorithm, and the tight association with molecular characteristics as well as tumor immune microenvironment was clarified. Sixteen prognostic factors were identified using univariate Cox regression analysis, and a 5mC regulator-based gene signature was further constructed via the least absolute shrinkage and selection operator (LASSO) cox analysis. This risk model was proved as an efficient predictor of overall survival for diffuse glioma, glioblastoma (GBM), and low-grade glioma (LGG) patients in three glioma cohorts. The significant correlation between risk score and intratumoral infiltrated immune cells, as well as immunosuppressive pathways, was found, which explained the difference in clinical outcomes between high and low-risk groups. Finally, a nomogram incorporating the gene signature and other clinicopathological risk factors was established, which might direct clinical decision making. In summary, our work highlights the potential clinical application value of 5mC regulators in prognostic stratification of glioma and their potentialities for developing novel treatment strategies.

cancer biology↗