High-coverage proteome analysis reveals the first insight of protein modification systems in the pathogenic spirochete Leptospira interrogans

Leptospirosis is a widespread zoonotic disease caused by pathogenic spirochetes of the genus Leptospira that infects humans and a wide range of animals. By combining computational prediction and high-accuracy tandem mass spectra, we revised the genome annotation of Leptospira interrogans serovar Lai, a free-living pathogenic spirochete responsible for leptospirosis, providing substantial peptide evidence for novel genes and new gene boundaries. Subsequently, we presented a high-coverage proteome analysis of protein expression and multiple posttranslational modifications （PTMs）. Approximately 64.3% of the predicted L. interrogans proteins were cataloged by detecting 2 540 proteins. Meanwhile, a profile of multiple PTMs was concurrently established, containing in total 32 phosphorylated, 46 acetylated and 155 methylated proteins. The PTM systems in the serovar Lai show unique features. Unique eukaryotic-like features of L. interrogans protein modifications were demonstrated in both phosphorylation and arginine methylation. This systematic analysis provides not only comprehensive information of high-coverage protein expression and multiple modifications in prokaryotes but also a view suggesting that the evolutionarily primitive L. interrogans shares significant similarities in protein modification systems with eukaryotes.

Research progress and prospects of arenavirus

Arenaviruses belong to the family of RNA viruses that can infect humans in various ways and cause different degrees of mortality.Rodents is the mainly hosts.Human pathogenic arenaviruses include lymphocytic choroid meningitis,Lassa virus group and Takarib virus group,which cause human lymphocytic choriomeningitis and human hemorrhagic diseases.Rodents account for about 43%of mammalian species.At present,more than 30 highly pathogenic viruses have been found in rodents,including arenaviruses.The arenaviridae that infects rodents are mainly mammalian arenaviruses.This article reviews the etiology,clinicopathology,epidemiology,prevention and control of arenavirus,and provides references for the research and prevention of arenavirus.

psk1 virulence gene-induced pulmonary and systemic tuberculosis in a young woman with normal immune function:A case report

BACKGROUND Tuberculosis is a chronic infectious disease and an important public health pro-blem.Despite progress in controlling tuberculosis,the incidence of tuberculosis in China is still very high,with 895000 new cases annually.This case report des-cribes the investigation of a case of severe disseminated tuberculosis in a young adult with normal immune function,conducted to ascertain why a Mycobacterium tuberculosis(M.tuberculosis)strain caused such severe disease.CASE SUMMARY A previously healthy 28-year-old woman presented to our hospital with a 1-mo-nth history of fever and fatigue.She was diagnosed with severe disseminated pulmonary tuberculosis,spinal tuberculosis with paravertebral abscesses,and tuberculous meningitis.M.tuberculosis was isolated from bronchoal-veolar lavage fluid.She was treated with standard antituberculous therapy and underwent debridement,bone graft,and internal fixation surgery for spinal tuberculosis.She responded to therapy and regained her ability to walk following the surgery.We analysed the whole-genome sequence of the strain and designated it BLM-A21.Additional M.tuberculosis genomes were selected from the Virulence Factor Database(http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=Mycobacterium)for comparison.An evolutionary tree of the BLM-A21 strain was built using PhyML maximum likelihood software.Further gene analysis revealed that,except for the pks1 gene,BLM-A21 had similar virulence genes to the CDC 1551 and H37Rv strains,which have lower dissemination.CONCLUSION We speculate that the pks1 virulence gene in BLM-A21 may be the key virulence gene responsible for the wide-spread dissemination of M.tuberculosis infection in this previously healthy adult with normal immune function.

Application of Nanopore Sequencing Technology in the Clinical Diagnosis of Infectious Diseases

Infectious diseases are an enormous public health burden and a growing threat to human health worldwide.Emerging or classic recurrent pathogens,or pathogens with resistant traits,challenge our ability to diagnose and control infectious diseases.Nanopore sequencing technology has the potential to enhance our ability to diagnose,interrogate,and track infectious diseases due to the unrestricted read length and system portability.This review focuses on the application of nanopore sequencing technology in the clinical diagnosis of infectious diseases and includes the following:(i)a brief introduction to nanopore sequencing technology and Oxford Nanopore Technologies(ONT)sequencing platforms;(ii)strategies for nanopore-based sequencing technologies;and(iii)applications of nanopore sequencing technology in monitoring emerging pathogenic microorganisms,molecular detection of clinically relevant drug-resistance genes,and characterization of disease-related microbial communities.Finally,we discuss the current challenges,potential opportunities,and future outlook for applying nanopore sequencing technology in the diagnosis of infectious diseases.

Bioinformatic analysis of chromatin organization and biased expression of duplicated genes between two poplars with a common whole-genome duplication

The nonrandom three-dimensional organization of chromatin plays an important role in the regulation of gene expression.However,it remains unclear whether this organization is conserved and whether it is involved in regulating gene expression during speciation after whole-genome duplication(WGD)in plants.In this study,high-resolution interaction maps were generated using high-throughput chromatin conformation capture(Hi-C)techniques for two poplar species,Populus euphratica and Populus alba var.pyramidalis,which diverged~14 Mya after a common WGD.We examined the similarities and differences in the hierarchical chromatin organization between the two species,including A/B compartment regions and topologically associating domains(TADs),as well as in their DNA methylation and gene expression patterns.We found that chromatin status was strongly associated with epigenetic modifications and gene transcriptional activity,yet the conservation of hierarchical chromatin organization across the two species was low.The divergence of gene expression between WGD-derived paralogs was associated with the strength of chromatin interactions,and colocalized paralogs exhibited strong similarities in epigenetic modifications and expression levels.Thus,the spatial localization of duplicated genes is highly correlated with biased expression during the diploidization process.This study provides new insights into the evolution of chromatin organization and transcriptional regulation during the speciation process of poplars after WGD.

Characterization of dwarf mutants and molecular mapping of a dwarf locus in soybean

Plant height is one of the most important traits in soybean. The semi-dwarf soybean cultivars could improve the ability of lodging resistance to obtain higher yield. To broaden the dwarfism germplasm resources in soybean, 44 dwarf mutants were identified from a gamma rays mutagenized M-2 population. Two of these mutants, Gmdwf1（Glycine max dwarf 1） and Gmdwf2（Glycine max dwarf 2）, were investigated in this study. Genetic analysis showed that both mutants were inherited in a recessive manner and their mutated regions were delimited to a 2.610-Mb region on chromosome 1 by preliminary mapping. Further fine mapping study proved that the two mutants had a common deletion region of 1.552 Mb in the target region, which was located in a novel locus site without being reported previously. The dwarfism of Gmdwf1 could not be rescued by gibberellin（GA） and brassinolide（BR） treatments, which indicated that the biosynthesis of these hormones was not deficient in Gmdwf1.

Temporal and spatial profiling of nuclei-associated proteins upon TNF-α/NF-kB signaling

The tumor necrosis factor （TNF）-α/NF-kB-signaling pathway plays a pivotal role in various processes including apoptosis, cellular differentiation, host defense, inflammation, autoimmunity and organogenesis. The complexity of the TNF-α/NF-kB signaling is in part due to the dynamic protein behaviors of key players in this pathway. In this present work, a dynamic and global view of the signaling components in the nucleus at the early stages of TNF-a/ NF-KB signaling was obtained in HEK293 cells, by a combination of subcellular fractionation and stable isotope la- beling by amino acids in cell culture （SILAC）. The dynamic profile patterns of 547 TNF-α-induced nuclei-associated proteins were quantified in our studies. The functional characters of all the profiles were further analyzed using that Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway annotation. Additionally, many previously unknown effectors of TNF-α/NF-kB signaling were identified, quantified and clustered into differential activation profiles. In- terestingly, levels of Fanconi anemia group D2 protein （FANCD2）, one of the Fanconi anemia family proteins, was found to be increased in the nucleus by SILAC quantitation upon TNF-α stimulation, which was further verified by western blotting and immunofluorescence analysis. This indicates that FANCD2 might be involved in TNF-α/NF-kB signaling through its accumulation in the nucleus. In summary, the combination of subcellular proteomics with quan- titative analysis not only allowed for a dissection of the nuclear TNF-α/NF-kB-signaling pathway, but also provided a systematic strategy for monitoring temporal and spatial changes in cell signaling.

Application of next generation sequencing technology on contamination monitoring in microbiology laboratory

The surveillance and prevention of pathogenic microbiological contamination are the most important tasks of biosafety management in the lab.There is an urgent need to establish an effective and unbiased method to evaluate and monitor such contamination.This study aims to investigate the utility of next generation sequencing(NGS)method to detect possible contamination in the microbiology laboratory.Environmental samples were taken at multiple sites at the lab including the inner site of centrifuge rotor,the bench used for molecular biological tests,the benches of biosafety cabinets used for viral culture,clinical sample pre-treatment and nucleic acids extraction,by scrubbing the sites using sterile flocked swabs.The extracted total nucleic acids were used to construct the libraries for deep sequencing according to the protocol of Ion Torrent platform.At least 1G raw data was obtained for each sample.The reads of viruses and bacteria accounted for 0.01±0.02%,and 77.76±12.53%of total reads respectively.The viral sequences were likely to be derived from gene amplification products,the nucleic acids contaminated in fetal bovine serum.Reads from environmental microorganisms were also identified.Our results suggested that NGS method was capable of monitoring the nucleic acids contaminations from different sources in the lab,demonstrating its promising utility in monitoring and assessing the risk of potential laboratory contamination.The risk of contamination from reagents,remnant DNA and environment should be considered in data analysis and results interpretation.

Identification of novel small-molecule inhibitors of SARS-CoV-2 by chemical genetics

There are only eight approved small molecule antiviral drugs for treating COVID-19.Among them,four are nucleotide analogues(remdesivir,JT001,molnupiravir,and azvudine),while the other four are protease inhibitors(nirmatrelvir,ensitrelvir,leritrelvir,and simnotrelvir-ritonavir).Antiviral resistance,unfavourable drug‒drug interaction,and toxicity have been reported in previous studies.Thus there is a dearth of new treatment options for SARS-CoV-2.In this work,a three-tier cell-based screening was employed to identify novel compounds with anti-SARS-CoV-2 activity.One compound,designated 172,demonstrated broad-spectrum antiviral activity against multiple human pathogenic coronaviruses and different SARS-CoV-2 variants of concern.Mechanistic studies validated by reverse genetics showed that compound 172 inhibits the 3-chymotrypsin-like protease(3CLpro)by binding to an allosteric site and reduces 3CLpro dimerization.A drug synergistic checkerboard assay demonstrated that compound 172 can achieve drug synergy with nirmatrelvir in vitro.In vivo studies confirmed the antiviral activity of compound 172 in both Golden Syrian Hamsters and K18 humanized ACE2 mice.Overall,this study identified an alternative druggable site on the SARS-CoV-23CLpro,proposed a potential combination therapy with nirmatrelvir to reduce the risk of antiviral resistance and shed light on the development of allosteric protease inhibitors for treating a range of coronavirus diseases.

Development and performance evaluation of a culture-independent nanopore amplicon-based sequencing method for accurate typing and antimicrobial resistance profiling in Neisseria gonorrhoeae

Dear Editor,Bacterial antimicrobial resistance(AMR)poses a serious threat to global human health(Antimicrobial Resistance Collaborators,2022).Comprehensive profiling of AMR and accurate molecular typing are important for tracking and controlling the emergence and dissemination of antibiotic-resistant bacteria(Yahara et al.,2021).We previously developed a multiplex amplicon sequencing-based method for directly sequencing AMR-related loci in N.gonorrhoeae from clinical samples(Zhang et al.,2021).

Impact of corticosteroids on initiation and half-year durability of humoral response in COVID-19 survivors

Background:The impact of corticosteroids on humoral responses in coronavirus disease 2019(COVID-19)sur-vivors during the acute phase and subsequent 6-month period remains unknown.This study aimed to determine how the use of corticosteroids influences the initiation and duration of humoral responses in COVID-19 survivors 6 months after infection onset.Methods:We used kinetic antibody data from the lopinavir-ritonavir trial conducted at Jin Yin-Tan Hospital in January 2020,which involved adults hospitalized with severe COVID-19(LOTUS,ChiCTR2000029308).Anti-body samples were collected from 192 patients during hospitalization,and kinetic antibodies were monitored at all available time points after recruitment.Additionally,plasma samples were collected from 101 COVID-19 survivors for comprehensive humoral immune measurement at the half-year follow-up visit.The main focus was comparing the humoral responses between patients treated with systemic corticosteroid therapy and the non-corticosteroid group.Results:From illness onset to day 30,the median antibody titre areas under the receiver operating characteristic curve(AUCs)of nucleoprotein(N),spike protein(S),and receptor-binding domain(RBD)immunoglobulin G(IgG)were significantly lower in the corticosteroids group.The AUCs of N-,S-,and RBD-IgM as well as neutralizing antibodies(NAbs)were numerically lower in the corticosteroids group compared with the non-corticosteroid group.However,peak titres of N,S,RBD-IgM and-IgG and NAbs were not influenced by corticosteroids.During 6-month follow-up,we observed a delayed decline for most binding antibodies,except N-IgM(𝛽−0.05,95%CI[−0.10,0.00])in the corticosteroids group,though not reaching statistical significance.No significant difference was observed for NAbs.However,for the half-year seropositive rate,corticosteroids significantly accelerated the decay of IgA and IgM but made no difference to N-,S-,and RBD-IgG or NAbs.Additionally,corticosteroids group showed a trend towards delayed viral clearance compared with the non-corticosteroid group,but the results were not statistically significant(adjusted hazard ratio 0.71,95%CI 0.50-1.00;P=0.0508).Conclusion:Our findings suggested that corticosteroid therapy was associated with impaired initiation of the antibody response but this did not compromise the peak titres of binding and neutralizing antibodies.Throughout the decay phase,from the acute phase to the half-year follow-up visit,short-term and low-dose corticosteroids did not significantly affect humoral responses,except for accelerating the waning of short-lived antibodies.

Adipogenesis licensing and execution are disparately linked to cell proliferation

Coordination of cell differentiation and proliferation is a key issue in the development process of multi-cellular organisms and stem cells. Here we provide evidence that the establishment of adipocyte differentiation of 3T3-L1 cells requires two processes： the licensing of an adipogenesis gene-expression program within a particular growth-arrest stage, i.e., the contact-inhibition stage, and then the execution of this program in a cell-cycle-independent manner, by which the licensed progenitors are differentiated into adipocytes in the presence of inducing factors. Our results showed that differentiation licensing of 3T3-L1 cells during the contact-inhibition stage involved epigenetic modifications such as DNA methylation and histone modifications, whereas disturbing these epigenetic modifications by DNA methylation inhibitors or RNAi during the contact-inhibition stage significantly reduced adipogenesis efficiency. More importantly, when these licensed 3T3-L1 cells were re-cultured under non-differentiating conditions or treated only with insulin, this adipogenesis commitment could be maintained from one cell generation to the next, whereby the licensed program could be activated in a cell-cycle-independent manner once these cells were subjected to adipo- genesis-inducing conditions. This result suggests that differentiation licensing and differentiation execution can be uncoupled and disparately linked to cell proliferation. Our findings deliver a new concept that cell-fate decision can be subdivided into at least two stages, licensing and execution, which might have different regulatory relationships with cell proliferation. In addition, this new concept may provide a clue for developing new strategies against obesity.

Reconstructing gene regulatory networks in single-cell transcriptomic data analysis

Gene regulatory networks play pivotal roles in our understanding of biological processes/mechanisms at the molecular level.Many studies have developed sample-specific or cell-type-specific gene regulatory networks from single-cell transcriptomic data based on a large amount of cell samples.Here,we review the state-of-the-art computational algorithms and describe various applications of gene regulatory networks in biological studies.

Bcl-2 cleavages at two adjacent sites by different caspases promote cisplatin-induced apoptosis

The protein encoded by bcl-2 proto-oncogene plays an important role in the mitochondria-mediated apoptotic pathway. Although the general role of Bcl-2 is anti-apoptotic, previous work showed that Bcl-2 fragments cleaved by caspases could promote apoptotic process. We report herein that Bcl-2 protein was cleaved to produce two fragments of around 23 kDa in human hepatocarcinoma BEL-7404 cells or in Bcl-2 overexpressing CHO cells induced by cisplatin. Treating cells with the general caspase inhibitor z-VAD-fmk blocked the induced cleavage of Bcl-2. Mutagenesis analyses showed that Bcl-2 was cleaved by caspases at two adjacent recognition sites in the loop domain （YEWD31↓AGD34↓V）, which could be inhibited by caspase-8 and -3 inhibitors, respectively. Overexpression of the carboxyl terminal 23 kDa fragments increased the sensitivity of CHO cells to cisplatin-induced apoptosis. These results indicate that Bcl-2 can be cleaved into two close fragments by different caspases during cisplatin-induced apoptosis, both of which contribute to the acceleration ofapoptotic process.

Host restriction factors for hepatitis C virus

Host-hepatitis C virus(HCV) interactions have both informed fundamental concepts of viral replication and pathogenesis and provided novel insights into host cell biology. These findings are illustrated by the recent discovery of host-encoded factors that restrict HCV infection. In this review, we briefly discuss these restriction factors in different steps of HCV infection. In each case, we discuss how these restriction factors were identified, the mechanisms by which they inhibit HCV infection and their potential contribution to viral pathogenesis.

Identification of Key Genes for the Ultrahigh Yield of Rice Using Dynamic Cross-tissue Network Analysis

Significantly increasing crop yield is a major and worldwide challenge for food supply and security.It is well-known that rice cultivated at Taoyuan in Yunnan of China can produce the highest yield worldwide.Yet,the gene regulatory mechanism underpinning this ultrahigh yield has been a mystery.Here,we systematically collected the transcriptome data for seven key tissues at different developmental stages using rice cultivated both at Taoyuan as the case group and at another regular rice planting place Jinghong as the control group.We identified the top 24 candidate high-yield genes with their network modules from these well-designed datasets by developing a novel computational systems biology method,i.e.,dynamic cross-tissue(DCT)network analysis.We used one of the candidate genes,Os SPL4,whose function was previously unknown,for gene editing experimental validation of the high yield,and confirmed that Os SPL4 significantly affects panicle branching and increases the rice yield.This study,which included extensive field phenotyping,cross-tissue systems biology analyses,and functional validation,uncovered the key genes and gene regulatory networks underpinning the ultrahigh yield of rice.The DCT method could be applied to other plant or animal systems if different phenotypes under various environments with the common genome sequences of the examined sample.DCT can be downloaded from https://github.com/ztpub/DCT.

Computational systems biology for omics data analysis

Recent trend on biological data at a molecular level is omics data analysis for both bulk and single cells, in eluding genomics, proteomics, metabolomics, and epigenetics data (Wang and Zhang, 2017;Zhang et al., 2017;Zhao and Li, 2017;Cheng and Leung, 2018). Rapid accumulation of such high-dimensional biological data is driving the system-level study from describing complex phenomena to understanding molecular mechanisms (Park et al., 2018;Sun et al., 2018) and from analyzi ng in dividual components to understanding their networks and systems (Chen et al., 2009;Chen, 2017).

TRAF3 activates STING-mediated suppression of EV-A71 and target of viral evasion

Innate immunity represents one of the main host responses to viral infection.1,2,3 STING(Stimulator of interferon genes),a crucial immune adapter functioning in host cells,mediates cGAS(Cyclic GMP-AMP Synthase)sensing of exogenous and endogenous DNA fragments and generates innate immune responses.4 Whether STING activation was involved in infection and replication of enterovirus remains largely unknown.In the present study,we discovered that human enterovirus A71(EV-A71)infection triggered STING activation in a cGAS dependent manner.EV-A71 infection caused mitochondrial damage and the discharge of mitochondrial DNA into the cytosol of infected cells.However,during EV-A71 infection,cGAS-STING activation was attenuated.EV-A71 ^(pro)teins were screened and the viral ^(pro)tease 2A^(pro) had the greatest capacity to inhibit cGAS-STING activation.We identified TRAF3 as an important factor during STING activation and as a target of 2A^(pro).Supplement of TRAF3 rescued cGAS-STING activation suppression by 2A^(pro).TRAF3 supported STING activation mediated TBK1 phosphorylation.Moreover,we found that 2A^(pro) ^(pro)tease activity was essential for inhibiting STING activation.Furthermore,EV-D68 and CV-A16 infection also triggered STING activation.The viral ^(pro)tease 2A^(pro) from EV-D68 and CV-A16 also had the ability to inhibit STING activation.As STING activation prior to EV-A71 infection generated cellular resistance to EV-A71 replication,blocking EV-A71-mediated STING suppression represents a new anti-viral target.

Single-Exosome Profiling Identifies ITGB3+and ITGAM+Exosome Subpopulations as Promising Early Diagnostic Biomarkers and Therapeutic Targets for Colorectal Cancer

Tumor metastasis is a hallmark of colorectal cancer(CRC),in which exosome plays a crucial role with its function in intercellular communication.Plasma exosomes were collected from healthy control(HC)donors,localized primary CRC and liver-metastatic CRC patients.We performed proximity barcoding assay(PBA)for single-exosome analysis,which enabled us to identify the alteration in exosome subpopulations associated with CRC progression.By in vitro and in vivo experiments,the biological impact of these subpopulations on cancer proliferation,migration,invasion,and metastasis was investigated.The potential application of exosomes as diagnostic biomarkers was evaluated in 2 independent validation cohorts by PBA.Twelve distinct exosome subpopulations were determined.We found 2 distinctly abundant subpopulations:one ITGB3-positive and the other ITGAM-positive.The ITGB3-positive cluster is rich in liver-metastatic CRC,compared to both HC group and primary CRC group.On the contrary,ITGAM-positive exosomes show a large-scale increase in plasma of HC group,compared to both primary CRC and metastatic CRC groups.Notably,both discovery cohort and validation cohort verified ITGB3+exosomes as potential diagnostic biomarker.ITGB3+exosomes promote proliferation,migration,and invasion capability of CRC.In contrast,ITGAM+exosomes suppress CRC development.Moreover,we also provide evidence that one of the sources of ITGAM+exosomes is macrophage.ITGB3+exosomes and ITGAM+exosomes are proven 2 potential diagnostic,prognostic,and therapeutic biomarkers for management of CRC.

Discovery and characterization of novel paramyxoviruses from bat samples in China

Many paramyxoviruses are responsible for a variety of mild to severe human and animal diseases.Based on the novel discoveries over the past several decades,the family Paramyxoviridae infecting various hosts across the world includes 4 subfamilies,17 classified genera and 78 species now.However,no systematic surveys of bat paramyxoviruses are available from the Chinese mainland.In this study,13,064 samples from 54 bat species were collected and a comprehensive paramyxovirus survey was conducted.We obtained 94 new genome sequences distributed across paramyxoviruses from 22 bat species in seven provinces.Bayesian phylodynamic and phylogenetic analyses showed that there were four different lineages in the Jeilongvirus genus.Based on available data,results of host and region switches showed that the bat colony was partial to interior,whereas the rodent colony was exported,and the felines and hedgehogs were most likely the intermediate hosts from Scotophilus spp.rather than rodents.Based on the evolutionary trend,genus Jeilongvirus may have originated from Mus spp.in Australia,then transmitted to bats and rodents in Africa,Asia and Europe,and finally to bats and rodents in America.