Objective To explore the relationship between human cytomegalovirus (HCMV) UL144 sequence variability and clinical disease. Methods HCMV UL144 open reading frame (ORF) was amplified by PCR assay in 72 lowpassage isola...Objective To explore the relationship between human cytomegalovirus (HCMV) UL144 sequence variability and clinical disease. Methods HCMV UL144 open reading frame (ORF) was amplified by PCR assay in 72 lowpassage isolates [65 con-genitally infective children and 7 healthy children who were HCMV-DNA positive by quantitative PCR (qPCR)]. All positive PCR products were analyzed by heteroduplex mobility assay and single-stranded conformation polymorphism (HMA-SSCP) and 32 of them were sequenced. Results Fifty-five patient isolates and five healthy children isolates were HCMV-UL144 positive by PCR. Sequencing and HMA-SSCP analysis showed that significant strain-specific variability was present in the UL144 ORF. Phylogenetic analysis indicated that the nucleotide sequences could be separated into 3 major genotypes. Comparing between UL144 se-quences and the corresponding symptoms showed that genotype 2 did not exist in megacolon isolates. And genotype 1 and 3 were the major types among microcephaly and jaundice isolates respectively. Conclusions HCMV-UL144 existed in most of low passage isolates and sequences were hypervariable. The UL144 ORF and its predicted product with the high level of sequence variability in different kinds of isolates suggest that UL144 ORF might play a role in HCMV infectivity and subsequent diseases.展开更多
The hepatitis E virus(HEV),a member of the Hepeviridae family,is a small,non-enveloped icosahedral virus divided into eight distinct genotypes(HEV-1 to HEV-8).Only genotypes 1 to 4 are known to cause diseases in human...The hepatitis E virus(HEV),a member of the Hepeviridae family,is a small,non-enveloped icosahedral virus divided into eight distinct genotypes(HEV-1 to HEV-8).Only genotypes 1 to 4 are known to cause diseases in humans.Genotypes 1 and 2 commonly spread via fecal-oral transmission,often through the consum-ption of contaminated water.Genotypes 3 and 4 are known to infect pigs,deer,and wild boars,often transferring to humans through inadequately cooked meat.Acute hepatitis caused by HEV in healthy individuals is mostly asymptomatic or associated with minor symptoms,such as jaundice.However,in immunosup-pressed individuals,the disease can progress to chronic hepatitis and even escalate to cirrhosis.For pregnant women,an HEV infection can cause fulminant liver failure,with a potential mortality rate of 25%.Mortality rates also rise amongst cirrhotic patients when they contract an acute HEV infection,which can even trigger acute-on-chronic liver failure if layered onto pre-existing chronic liver disease.As the prevalence of HEV infection continues to rise worldwide,highlighting the particular risks associated with severe HEV infection is of major medical interest.This text offers a brief summary of the characteristics of hepatitis developed by patient groups at an elevated risk of severe HEV infection.展开更多
AIM: To isolate a novel isoform of human HPO (HPO-205) from human fetal liver Marathon-ready cDNA and characterize its primary biological function. METHODS: 5'-RACE (rapid amplification of cDNA 5' ends) was us...AIM: To isolate a novel isoform of human HPO (HPO-205) from human fetal liver Marathon-ready cDNA and characterize its primary biological function. METHODS: 5'-RACE (rapid amplification of cDNA 5' ends) was used to isolate a novel isoform of hHPO in this paper. The constructed pcDNA(HPO-205), pcDNA(HPO) and pcDNA eukaryotic expression vectors were respectively transfected by lipofectamine method and the stimulation of DNA synthesis was observed by (3)H-TdR incorporation assay. Proteins extracted from different cells were analyzed by Western blot. RESULTS: A novel isoform of hHPO (HPO-205) encoding a 205 amino acid ORF corresponding to a translated production of 23 kDa was isolated and distinguished from the previous HPO that lacked the N-terminal 80 amino acids. The dose-dependent stimulation of DNA synthesis of HepG2 hepatoma cells by HPO-205 demonstrated its similar biological activity with HPO in vitro. The level of MAPK (Mitogen-activated protein kinase) phosphorylation by Western blot analysis revealed that HPO-205 might have the stronger activity of stimulating hepatic cell proliferation than that of HPO. CONCLUSION: A novel isoform of hHPO (HPO-205) was isolated from hepatic-derived cells. The comparison of HPO-205 and HPO will lead to a new insight into the structure and function of hHPO, and provide the new way of thinking to deeply elucidate the biological roles of HPO/ALR.展开更多
AIM： To construct the plasmid pcHEV23 containing fragments of HEV ORF2 and ORF3 chimeric gene and to assess its ability to elicit specific immunologic response in mice. METHODS： The gene encoding the structural prot...AIM： To construct the plasmid pcHEV23 containing fragments of HEV ORF2 and ORF3 chimeric gene and to assess its ability to elicit specific immunologic response in mice. METHODS： The gene encoding the structural protein of HEV ORF2 fragment and full-length ORF3 was amplified by PCR. The PCR products were cloned into an eucaryotic expression plasmid pcDNA3. The resulting plasmid pcHEV23 was used as a DNA vaccine to inoculate BALB/c mice intramuscularly thrice at a dose of 100 or 200 ug. Mice injected with empty pcDNA3 DNA or saline served as control and then specific immune responses in the mice were detected. RESULTS： After 2-3 times of inoculation, all mice injected with pcHEV23 had anti-HEV IgG seroconversion and specific T lymphocyte proliferation. The lymphocyte stimulation index in the group immunized with pcHEV23 （3.1＋0.49） was higher than that in the control group （0.787±0.12, P〈0.01）. None in the control group had a detectable level of anti-HEV IgG. CONCLUSION： DNA vaccine containing HEV ORF2 and ORF3 chimeric gene can successfully induce specific humoral and cellular immune response in mice.展开更多
This paper reports the confirmed diagnosis by nested RT-PCR of PPR cases in Tibet, China in 2007, and results of phylogenetic analysis. Results showed that the 11 tested samples were PPRV positive by nested RT-PCR, of...This paper reports the confirmed diagnosis by nested RT-PCR of PPR cases in Tibet, China in 2007, and results of phylogenetic analysis. Results showed that the 11 tested samples were PPRV positive by nested RT-PCR, of which 2 samples were genetically close to the X7443 strain (Nigeria 75/1) of lineage I, and 3 samples close to the strain AY560591 (Sungri96) of linage IV with 96.6%、97.3%、97.6% and 98% nucleotide sequence homogeneity respectively, based on partial sequencing of the F gene from 5 samples and complete sequencing of the N/M/F/H genes from one sample. This study suggested that there are at least 2 origins of PPRV in China.展开更多
Fibroblast growth factor (FGF) is a key regulator of developmental processes. A FGF homolog (vFGF) is found in all lepidopteran baculoviruses. Autographa californica nucleopolyhedrovirus (AcMNPV) and Bombyx mori NPV (...Fibroblast growth factor (FGF) is a key regulator of developmental processes. A FGF homolog (vFGF) is found in all lepidopteran baculoviruses. Autographa californica nucleopolyhedrovirus (AcMNPV) and Bombyx mori NPV (BmNPV) vFGFs are chemotactic factors. Here we analyzed the vfgf of Helicoverpa armigera NPV (HearNPV), a group II NPV. The HearNPV vfgf transcripts were detected from 18 to 96 h post-infection (hpi) of Hz-AM1 cells with HearNPV and encoded a 36 kDa protein, which was secreted into the culture medium. HearNPV vFGF had strong affinity to heparin, a property important for FGF signaling via an FGF receptor. Unlike its AcMNPV homolog, HearNPV vFGF specially chemoattracted Hz-AM1, but not other insect cells such as Sf9 and Se-UCR and not the mammalian cells 293 and HepG2. HearNPV vFGF is also associated with the envelope of BV but is absent in occlusion-derived virus, which coordinated to the chemotatic activity analysis.展开更多
A single mammalian transcript normally encodes one protein, but the transcript of GNAS （G-protein u-subunit） contains two reading frames and produces two structurally unrelated proteins, XLas and ALEX. No other conf...A single mammalian transcript normally encodes one protein, but the transcript of GNAS （G-protein u-subunit） contains two reading frames and produces two structurally unrelated proteins, XLas and ALEX. No other confirmed GNAS-Iike dual-coding transcripts have been reported to date, even though many such candidate genes have been predicted by bioinformatics analysis. In this study, we constructed a series of vectors to test how two protein products were translated from a single transcript in vitro. The length of the ORF （open reading frame）, position of the first AUG and the Kozak motif were found to be important factors. These factors, as well as 55-bp NMD （nonsense-mediated mRNA decay） rule, were used in a bioinformatics search for candidate dual-coding transcripts. A total of 1307, 750 and 474 two-ORF-containing transcripts were found in human, mouse and rat, respectively, of which 170, 89 and 70, respectively, were found to be potential dual-coding transcripts. Most transcripts showed low conservation among species. Interestingly, dual-coding transcripts were significantly enriched for transcripts from the zinc-finger protein family, which are usually DNA-binding proteins involved in regulation of the transcription process.展开更多
AIMTo investigate the role of non-structural open reading frame 1 “Y-domain” sequences in the hepatitis E virus (HEV) life cycle.METHODSSequences of human HEV Y-domain (amino acid sequences 216...AIMTo investigate the role of non-structural open reading frame 1 “Y-domain” sequences in the hepatitis E virus (HEV) life cycle.METHODSSequences of human HEV Y-domain (amino acid sequences 216-442) and closely-related viruses were analyzed in silico. Site-directed mutagenesis of the Y-domain (HEV SAR55) was carried out and studied in the replicon-baculovirus-hepatoma cell model. In vitro transcribed mRNA (pSK-GFP) constructs were transfected into S10-3 cells and viral RNA replicating GFP-positive cells were scored by flow cytometry. Mutant virions’ infectivity was assayed on naïve HepG2/C3A cells.RESULTSIn silico analysis identified a potential palmitoylation-site (C<sub>336</sub>C<sub>337</sub>) and an α-helix segment (L<sub>410</sub>Y<sub>411</sub>S<sub>412</sub>W<sub>413</sub>L<sub>414</sub>F<sub>415</sub>E<sub>416</sub>) in the HEV Y-domain. Molecular characterization of C<sub>336</sub>A, C<sub>337</sub>A and W<sub>413</sub>A mutants of the three universally conserved residues showed non-viability. Further, of the 10 consecutive saturation mutants covering the entire Y-domain nucleotide sequences (nts 650-1339), three constructs (nts 788-994) severely affected virus replication. This revealed the indispensability of the internal sequences but not of the up- or downstream sequences at the transcriptional level. Interestingly, the three mutated residues corresponded to the downstream codons that tolerated saturation mutation, indicating their post-translational functional/structural essentiality. In addition, RNA secondary structure prediction revealed formation of stable hairpins (nts 788-994) where saturation mutation drastically inhibited virion infectivity.CONCLUSIONThis is the first demonstration of the critical role of Y-domain sequences in HEV life cycle, which may involve gene regulation and/or membrane binding in intracellular replication complexes.展开更多
OBJECTIVE: To obtain recombinant antigen for development of anti-HEV ELISA kit and vaccine against hepatitis E virus infection. METHODS: A 492 base cDNA was collected from 5'-terminus of open reading frame 2 (ORF2...OBJECTIVE: To obtain recombinant antigen for development of anti-HEV ELISA kit and vaccine against hepatitis E virus infection. METHODS: A 492 base cDNA was collected from 5'-terminus of open reading frame 2 (ORF2) among epidemic hepatitis E virus (HEV) isolated from Xinjiang, Western China. The fragment was digested with BamH I and EcoR I, and inserted into vector pGEX-4T-3 which was also digested by the same enzyme. The recombinant plasmid was transformed into E. coli TG-1 and the fusion protein expressed was confirmed by Western blot analysis using serum of a patient with hepatitis E. RESULTS: The recombinant plasmid was identified and confirmed with enzyme digestion, polymerase chain reaction (PCR) and sequencing, respectively. A protein band of about 46 kDa was demonstrated by SDS-PAGE and designated GST-pORF2. The result of Western blot analysis suggested that the fusion protein reacted with anti-HEV positive sera at a dilution of 1:100. CONCLUSION: The recombinant protein GST-pORF2 may be useful in developing anti-HEV ELISA kit and vaccine against hepatitis E virus infection.展开更多
In the present study, 89 porcine reproductive and respiratory syndrome virus(PRRSV) isolates in China during 2007 to 2012 were randomly selected from the GenBank genetic sequence database. Evolutionary characteristics...In the present study, 89 porcine reproductive and respiratory syndrome virus(PRRSV) isolates in China during 2007 to 2012 were randomly selected from the GenBank genetic sequence database. Evolutionary characteristics of these isolates were analyzed based on the sequences of non-struc-tural protein 2(Nsp2) and glycoprotein 5(GP5). The genetic variations of the isolates were also compared with six representative strains. The results showed that a high degree of genetic diversity exists among the PRRSV population in China. Highly pathogenic PRRSV isolates, with a discon-tinuous deletion of a 30 amino acid residue in the Nsp2 region, remained the most dominant virus throughout 2007–2012 in China. Owing to the extensive use of representative vaccine strains, natu-ral recombination events occurred between strains. Three isolates – HH08, DY, and YN-2011 – were more closely related to vaccine strains than the other isolates. Both YN-2011 and DY were the evolu-tionary products of recombination events between strains SP and CH-1R. The results of the present study provide useful information for the epidemiology of PRRSV as well as for vaccine development.展开更多
With the development of modern sequencing techniques and bioinformatics, genomes that were once thought to be noncoding have been found to encode abundant functional micropeptides(miPs), a kind of small polypeptides. ...With the development of modern sequencing techniques and bioinformatics, genomes that were once thought to be noncoding have been found to encode abundant functional micropeptides(miPs), a kind of small polypeptides. Although miPs are difficult to analyze and identify, a number of studies have begun to focus on them. More and more miPs have been revealed as essential for energy metabolism homeostasis, immune regulation, and tumor growth and development. Many reports have shown that miPs are especially essential for regulating glucose and lipid metabolism and regulating mitochondrial function.MiPs are also involved in the progression of related diseases. This paper reviews the sources and identification of miPs, as well as the functional significance of miPs for metabolism-related diseases, with the aim of revealing their potential clinical applications.展开更多
OBJECTIVE: To investigate the genotypes of hepatitis E viruses (HEV) detected in sera of patients from different regions of China. METHODS: The partial genome (nt6461-6860, nt5994-6294) of open reading frame 2 (ORF2) ...OBJECTIVE: To investigate the genotypes of hepatitis E viruses (HEV) detected in sera of patients from different regions of China. METHODS: The partial genome (nt6461-6860, nt5994-6294) of open reading frame 2 (ORF2) of 45 HEV strains detected from 14 cities of China was amplified and sequenced using polymerase chain reaction (PCR) and direct sequencing. RESULTS: Forty-one of 45 strains (91%) share the same genotype with HEV Burma strain (B), with nucleotide identities higher than 98% with the representative HEV Chinese strain. Only 4 HEV strains are significantly divergent from the 3 prototype strains of HEV, with nucleotide identities of 77%-80% with HEV Burmese/Chinese strain, 74%-76% with Mexican strain and 74%-77% with the newly discovered HEV US/swine strain, respectively. Phylogenetic analysis suggests that these 4 strains may represent 2 different subtypes that belong to a novel genotype of HEV, which is significantly divergent from the prototype Mexico, Burmese and US/swine strains. CONCLUSION: Among patients with hepatitis E in China, most are infected by the Chinese prototype HEV, and only a small part by the new genotype HEV.展开更多
Small proteins specifically refer to proteins consisting of less than 100 amino acids translated from small open reading frames(s ORFs),which were usually missed in previous genome annotation.The significance of small...Small proteins specifically refer to proteins consisting of less than 100 amino acids translated from small open reading frames(s ORFs),which were usually missed in previous genome annotation.The significance of small proteins has been revealed in current years,along with the discovery of their diverse functions.However,systematic annotation of small proteins is still insufficient.Sm Prot was specially developed to provide valuable information on small proteins for scientific community.Here we present the update of Sm Prot,which emphasizes reliability of translated s ORFs,genetic variants in translated s ORFs,disease-specific s ORF translation events or sequences,and remarkably increased data volume.More components such as non-ATG translation initiation,function,and new sources are also included.Sm Prot incorporated638,958 unique small proteins curated from 3,165,229 primary records,which were computationally predicted from 419 ribosome profiling(Ribo-seq)datasets or collected from literature and other sources from 370 cell lines or tissues in 8 species(Homo sapiens,Mus musculus,Rattus norvegicus,Drosophila melanogaster,Danio rerio,Saccharomyces cerevisiae,Caenorhabditis elegans,and Escherichia coli).In addition,small protein families identified from human microbiomes were also collected.All datasets in Sm Prot are free to access,and available for browse,search,and bulk downloads at http://bigdata.ibp.ac.cn/SmProt/.展开更多
Non-conventional peptides(NCPs),which include small open reading frame-encoded peptides,play critical roles in fundamental biological processes.In this study,we developed an integrated peptidogenomic pipeline using hi...Non-conventional peptides(NCPs),which include small open reading frame-encoded peptides,play critical roles in fundamental biological processes.In this study,we developed an integrated peptidogenomic pipeline using high-throughput mass spectra to probe a customized six-frame translation database and applied it to large-scale identification of NCPs in plants.A total of 1993 and 1860 NCPs were unambiguously identified in maize and Arabidopsis,respectively.These NCPs showed distinct characteristics compared with conventional peptides and were derived from introns,3′UTRs,5′UTRs,junctions,and intergenic regions.Furthermore,our results showed that translation events in unannotated transcripts occur more broadly than previously thought.In addition,we found that dozens of maize NCPs are enriched within regions associated with phenotypic variations and domestication selection,indicating that they potentially are involved in genetic regulation of complex traits and domestication in maize.Taken together,our study developed an integrated peptidogenomic pipeline for large-scale identification of NCPs in plants,which would facilitate global characterization of NCPs from other plants.The identification of large-scale NCPs in both monocot(maize)and dicot(Arabidopsis)plants indicates that a large portion of plant genome can be translated into biologically functional molecules,which has important implications for functional genomic studies.展开更多
Background DNA analysis has shown a lack of significant compatibility between couples affected by unexplained recurrent spontaneous abortion (URSA) compared with normal fertile couples, 8 although one study that ma...Background DNA analysis has shown a lack of significant compatibility between couples affected by unexplained recurrent spontaneous abortion (URSA) compared with normal fertile couples, 8 although one study that made use of a PCR-sequence-specific oligonucleotide (SSO) method did observe evidence of significant compatibility in the HLA-DQA1 and DQB1 alleles between patients and aborted fetuses. 9 This study was designed to investigate whether URSA were associated with particular DQ alleles or promoter alleles.Methods Thirty-two patients with URSA and 54 women who had had at least one successful pregnancy were included in this study. HLA-DQ genotyping was performed by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The HLA-DQB1 promoter was detected by the SSO and sequence-specific primer (SSP) methods. The DQA1, DQB1, and DQB1 promoter (QBP) gene frequencies in the patients were compared with the gene frequencies in normal controls. The data were analyzed statistically with the χ 2 and Fisher’s exact tests.Results The results showed that the frequency of DQB1 *0604/0605 was significantly higher and the frequency of DQB1 *0501/0502 was significantly lower in the patient group as compared with the normal controls. In addition, the frequencies of the DQA1 *01-DQB1 *0604/0605 and QBP6.2-DQB1 *0604/0605 haplotypes were overrepresented in the patients relative to the controls. Our results did not show any differences between URSA patients and the controls with regard to DQA1 and QBP allele frequencies. Conclusions Our data suggest that URSA is associated with the HLA-DQB1 coding region, and is not associated with its upstream regulatory region. The DQB1 *0604/0605, DQA1 *01-DQB1 *0604/0605, and QBP6.2-DQB1 *0604/0605 haplotypes may confer susceptibility to URSA, while the DQB1 *0501/0502 allele may protect women from URSA.展开更多
The outbreak of coronavirus disease 2019(COVID-19)in Wuhan,China,was caused by a novel coronavirus(CoV),named severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).The rapid detection of viral nucleic acids is c...The outbreak of coronavirus disease 2019(COVID-19)in Wuhan,China,was caused by a novel coronavirus(CoV),named severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).The rapid detection of viral nucleic acids is critical for the early identification of infected cases.We have developed two TaqMan real-time reverse transcription-PCR assays to detect SARS-CoV-2.The designed primers target the nucleocapsid(N)and open reading frame(ORF)1b gene regions,where the probes discriminate SARS-CoV-2 from other human and animal CoVs.The sensitivities are one genomic copy per reaction for theN gene assay and ten copies for the ORF 1b gene assay.The overall linear detection ranges are 1–10^(6)and 10–10^(6)copies per reaction for the N gene assay and the ORF 1b gene assay,respectively.Surveillance of 23 suspected COVID-19 patients demonstrated that SARS-CoV-2 could be detected from 100%(23/23)and 62.5%(16/23)of clinical specimens by the N gene assay and the ORF 1b gene assay,respectively.All of the samples not detected by the ORF 1b gene assay were throat swabs,indicating a lower viral load in the upper respiratory tract and the relatively lower sensitivity of the ORF 1b gene assay.The assays developed in the present study offer alternative diagnostic tests for COVID-19.展开更多
The GGGGCC(G_(4)C_(2))hexanucleotide repeat expansion in the C9ORF72 gene is a major cause of both hereditary amyotrophic lateral sclerosis and familial frontotemporal dementia.Recent studies have shown that G_(4)C_(2...The GGGGCC(G_(4)C_(2))hexanucleotide repeat expansion in the C9ORF72 gene is a major cause of both hereditary amyotrophic lateral sclerosis and familial frontotemporal dementia.Recent studies have shown that G_(4)C_(2)hexanucleotide repeat-containing RNA transcripts((G_(4)C_(2))_(n)RNA)could go through liquid-liquid phase separation to form RNA foci,which may elicit neurodegeneration.However,the direct causality between these abnormal RNA foci and neuronal toxicity remains to be demonstrated.Here we introduce an optogenetic control system that can induce the assembly and phase separation of(G_(4)C_(2))_(n)RNA foci with blue light illumination in human cells,by fusing a specific(G_(4)C_(2))_(n)RNA binding protein as the linker domain to Cry2,a protein that oligomerizes in response to blue light.Our results demonstrate that a higher number of G_(4)C_(2)repeats have the potential to be induced into more RNA foci in the cells.Both spontaneous and induced RNA foci display liquid-like properties according to FRAP measurements.Computational simulation shows strong consistency with the experimental results and supports the effect of our system to promote the propensity of(G_(4)C_(2))_(n)RNA towards phase separation.This system can thus be used to investigate whether(G_(4)C_(2))_(n)RNA foci would disrupt normal cellular processes and lead to pathological phenotypes relevant to repeat expansion disorders.展开更多
基金Supported by the National Natural Science Foundation of China (30170986).
文摘Objective To explore the relationship between human cytomegalovirus (HCMV) UL144 sequence variability and clinical disease. Methods HCMV UL144 open reading frame (ORF) was amplified by PCR assay in 72 lowpassage isolates [65 con-genitally infective children and 7 healthy children who were HCMV-DNA positive by quantitative PCR (qPCR)]. All positive PCR products were analyzed by heteroduplex mobility assay and single-stranded conformation polymorphism (HMA-SSCP) and 32 of them were sequenced. Results Fifty-five patient isolates and five healthy children isolates were HCMV-UL144 positive by PCR. Sequencing and HMA-SSCP analysis showed that significant strain-specific variability was present in the UL144 ORF. Phylogenetic analysis indicated that the nucleotide sequences could be separated into 3 major genotypes. Comparing between UL144 se-quences and the corresponding symptoms showed that genotype 2 did not exist in megacolon isolates. And genotype 1 and 3 were the major types among microcephaly and jaundice isolates respectively. Conclusions HCMV-UL144 existed in most of low passage isolates and sequences were hypervariable. The UL144 ORF and its predicted product with the high level of sequence variability in different kinds of isolates suggest that UL144 ORF might play a role in HCMV infectivity and subsequent diseases.
基金Supported by Interreg V-A Romania-Hungary Programme,No.ROHU339.
文摘The hepatitis E virus(HEV),a member of the Hepeviridae family,is a small,non-enveloped icosahedral virus divided into eight distinct genotypes(HEV-1 to HEV-8).Only genotypes 1 to 4 are known to cause diseases in humans.Genotypes 1 and 2 commonly spread via fecal-oral transmission,often through the consum-ption of contaminated water.Genotypes 3 and 4 are known to infect pigs,deer,and wild boars,often transferring to humans through inadequately cooked meat.Acute hepatitis caused by HEV in healthy individuals is mostly asymptomatic or associated with minor symptoms,such as jaundice.However,in immunosup-pressed individuals,the disease can progress to chronic hepatitis and even escalate to cirrhosis.For pregnant women,an HEV infection can cause fulminant liver failure,with a potential mortality rate of 25%.Mortality rates also rise amongst cirrhotic patients when they contract an acute HEV infection,which can even trigger acute-on-chronic liver failure if layered onto pre-existing chronic liver disease.As the prevalence of HEV infection continues to rise worldwide,highlighting the particular risks associated with severe HEV infection is of major medical interest.This text offers a brief summary of the characteristics of hepatitis developed by patient groups at an elevated risk of severe HEV infection.
基金the National Natural Science Foundation of China,No.39830440
文摘AIM: To isolate a novel isoform of human HPO (HPO-205) from human fetal liver Marathon-ready cDNA and characterize its primary biological function. METHODS: 5'-RACE (rapid amplification of cDNA 5' ends) was used to isolate a novel isoform of hHPO in this paper. The constructed pcDNA(HPO-205), pcDNA(HPO) and pcDNA eukaryotic expression vectors were respectively transfected by lipofectamine method and the stimulation of DNA synthesis was observed by (3)H-TdR incorporation assay. Proteins extracted from different cells were analyzed by Western blot. RESULTS: A novel isoform of hHPO (HPO-205) encoding a 205 amino acid ORF corresponding to a translated production of 23 kDa was isolated and distinguished from the previous HPO that lacked the N-terminal 80 amino acids. The dose-dependent stimulation of DNA synthesis of HepG2 hepatoma cells by HPO-205 demonstrated its similar biological activity with HPO in vitro. The level of MAPK (Mitogen-activated protein kinase) phosphorylation by Western blot analysis revealed that HPO-205 might have the stronger activity of stimulating hepatic cell proliferation than that of HPO. CONCLUSION: A novel isoform of hHPO (HPO-205) was isolated from hepatic-derived cells. The comparison of HPO-205 and HPO will lead to a new insight into the structure and function of hHPO, and provide the new way of thinking to deeply elucidate the biological roles of HPO/ALR.
基金Supported by the Grants from the Natural Science Foundation of Zhejiang Province, No. RC01054, Science Technology Department of Zhejiang Province, No. F11023 and Key Project of Health Bureau of Zhejiang Province
文摘AIM： To construct the plasmid pcHEV23 containing fragments of HEV ORF2 and ORF3 chimeric gene and to assess its ability to elicit specific immunologic response in mice. METHODS： The gene encoding the structural protein of HEV ORF2 fragment and full-length ORF3 was amplified by PCR. The PCR products were cloned into an eucaryotic expression plasmid pcDNA3. The resulting plasmid pcHEV23 was used as a DNA vaccine to inoculate BALB/c mice intramuscularly thrice at a dose of 100 or 200 ug. Mice injected with empty pcDNA3 DNA or saline served as control and then specific immune responses in the mice were detected. RESULTS： After 2-3 times of inoculation, all mice injected with pcHEV23 had anti-HEV IgG seroconversion and specific T lymphocyte proliferation. The lymphocyte stimulation index in the group immunized with pcHEV23 （3.1＋0.49） was higher than that in the control group （0.787±0.12, P〈0.01）. None in the control group had a detectable level of anti-HEV IgG. CONCLUSION： DNA vaccine containing HEV ORF2 and ORF3 chimeric gene can successfully induce specific humoral and cellular immune response in mice.
基金This work was supported by project from MOA [2006-G57(3)B-Z1] Project from Yunnan Province (2008LA019)
文摘This paper reports the confirmed diagnosis by nested RT-PCR of PPR cases in Tibet, China in 2007, and results of phylogenetic analysis. Results showed that the 11 tested samples were PPRV positive by nested RT-PCR, of which 2 samples were genetically close to the X7443 strain (Nigeria 75/1) of lineage I, and 3 samples close to the strain AY560591 (Sungri96) of linage IV with 96.6%、97.3%、97.6% and 98% nucleotide sequence homogeneity respectively, based on partial sequencing of the F gene from 5 samples and complete sequencing of the N/M/F/H genes from one sample. This study suggested that there are at least 2 origins of PPRV in China.
基金National Nature Science Foundations of China (30325002,30670077)National Basic Research Priorities Program of China (2003CB1140).
文摘Fibroblast growth factor (FGF) is a key regulator of developmental processes. A FGF homolog (vFGF) is found in all lepidopteran baculoviruses. Autographa californica nucleopolyhedrovirus (AcMNPV) and Bombyx mori NPV (BmNPV) vFGFs are chemotactic factors. Here we analyzed the vfgf of Helicoverpa armigera NPV (HearNPV), a group II NPV. The HearNPV vfgf transcripts were detected from 18 to 96 h post-infection (hpi) of Hz-AM1 cells with HearNPV and encoded a 36 kDa protein, which was secreted into the culture medium. HearNPV vFGF had strong affinity to heparin, a property important for FGF signaling via an FGF receptor. Unlike its AcMNPV homolog, HearNPV vFGF specially chemoattracted Hz-AM1, but not other insect cells such as Sf9 and Se-UCR and not the mammalian cells 293 and HepG2. HearNPV vFGF is also associated with the envelope of BV but is absent in occlusion-derived virus, which coordinated to the chemotatic activity analysis.
文摘A single mammalian transcript normally encodes one protein, but the transcript of GNAS （G-protein u-subunit） contains two reading frames and produces two structurally unrelated proteins, XLas and ALEX. No other confirmed GNAS-Iike dual-coding transcripts have been reported to date, even though many such candidate genes have been predicted by bioinformatics analysis. In this study, we constructed a series of vectors to test how two protein products were translated from a single transcript in vitro. The length of the ORF （open reading frame）, position of the first AUG and the Kozak motif were found to be important factors. These factors, as well as 55-bp NMD （nonsense-mediated mRNA decay） rule, were used in a bioinformatics search for candidate dual-coding transcripts. A total of 1307, 750 and 474 two-ORF-containing transcripts were found in human, mouse and rat, respectively, of which 170, 89 and 70, respectively, were found to be potential dual-coding transcripts. Most transcripts showed low conservation among species. Interestingly, dual-coding transcripts were significantly enriched for transcripts from the zinc-finger protein family, which are usually DNA-binding proteins involved in regulation of the transcription process.
基金Supported by the Deanship of Scientific Research at King Saud University,Riyadh,No.RG-1435-053
文摘AIMTo investigate the role of non-structural open reading frame 1 “Y-domain” sequences in the hepatitis E virus (HEV) life cycle.METHODSSequences of human HEV Y-domain (amino acid sequences 216-442) and closely-related viruses were analyzed in silico. Site-directed mutagenesis of the Y-domain (HEV SAR55) was carried out and studied in the replicon-baculovirus-hepatoma cell model. In vitro transcribed mRNA (pSK-GFP) constructs were transfected into S10-3 cells and viral RNA replicating GFP-positive cells were scored by flow cytometry. Mutant virions’ infectivity was assayed on naïve HepG2/C3A cells.RESULTSIn silico analysis identified a potential palmitoylation-site (C<sub>336</sub>C<sub>337</sub>) and an α-helix segment (L<sub>410</sub>Y<sub>411</sub>S<sub>412</sub>W<sub>413</sub>L<sub>414</sub>F<sub>415</sub>E<sub>416</sub>) in the HEV Y-domain. Molecular characterization of C<sub>336</sub>A, C<sub>337</sub>A and W<sub>413</sub>A mutants of the three universally conserved residues showed non-viability. Further, of the 10 consecutive saturation mutants covering the entire Y-domain nucleotide sequences (nts 650-1339), three constructs (nts 788-994) severely affected virus replication. This revealed the indispensability of the internal sequences but not of the up- or downstream sequences at the transcriptional level. Interestingly, the three mutated residues corresponded to the downstream codons that tolerated saturation mutation, indicating their post-translational functional/structural essentiality. In addition, RNA secondary structure prediction revealed formation of stable hairpins (nts 788-994) where saturation mutation drastically inhibited virion infectivity.CONCLUSIONThis is the first demonstration of the critical role of Y-domain sequences in HEV life cycle, which may involve gene regulation and/or membrane binding in intracellular replication complexes.
基金This study was supported by Natural Scientific Fund of China (No. 39670666), Outstanding Youth Fund of Zhejiang Province in Medicine, Science & Technology Project of Zhejiang Province, and Key Science & Technology Project of Zhejiang Province in Medicine
文摘OBJECTIVE: To obtain recombinant antigen for development of anti-HEV ELISA kit and vaccine against hepatitis E virus infection. METHODS: A 492 base cDNA was collected from 5'-terminus of open reading frame 2 (ORF2) among epidemic hepatitis E virus (HEV) isolated from Xinjiang, Western China. The fragment was digested with BamH I and EcoR I, and inserted into vector pGEX-4T-3 which was also digested by the same enzyme. The recombinant plasmid was transformed into E. coli TG-1 and the fusion protein expressed was confirmed by Western blot analysis using serum of a patient with hepatitis E. RESULTS: The recombinant plasmid was identified and confirmed with enzyme digestion, polymerase chain reaction (PCR) and sequencing, respectively. A protein band of about 46 kDa was demonstrated by SDS-PAGE and designated GST-pORF2. The result of Western blot analysis suggested that the fusion protein reacted with anti-HEV positive sera at a dilution of 1:100. CONCLUSION: The recombinant protein GST-pORF2 may be useful in developing anti-HEV ELISA kit and vaccine against hepatitis E virus infection.
基金supported by the Jilin Province Science and Technology Development Project(No.20140101123JC)the Fundamental Research Fund of Jilin Universitythe Program for Changjiang Scholars and Innovative Research Team in University(No.IRT1248)
文摘In the present study, 89 porcine reproductive and respiratory syndrome virus(PRRSV) isolates in China during 2007 to 2012 were randomly selected from the GenBank genetic sequence database. Evolutionary characteristics of these isolates were analyzed based on the sequences of non-struc-tural protein 2(Nsp2) and glycoprotein 5(GP5). The genetic variations of the isolates were also compared with six representative strains. The results showed that a high degree of genetic diversity exists among the PRRSV population in China. Highly pathogenic PRRSV isolates, with a discon-tinuous deletion of a 30 amino acid residue in the Nsp2 region, remained the most dominant virus throughout 2007–2012 in China. Owing to the extensive use of representative vaccine strains, natu-ral recombination events occurred between strains. Three isolates – HH08, DY, and YN-2011 – were more closely related to vaccine strains than the other isolates. Both YN-2011 and DY were the evolu-tionary products of recombination events between strains SP and CH-1R. The results of the present study provide useful information for the epidemiology of PRRSV as well as for vaccine development.
基金supported by the National Natural Science Foundation of China(No.81870237)。
文摘With the development of modern sequencing techniques and bioinformatics, genomes that were once thought to be noncoding have been found to encode abundant functional micropeptides(miPs), a kind of small polypeptides. Although miPs are difficult to analyze and identify, a number of studies have begun to focus on them. More and more miPs have been revealed as essential for energy metabolism homeostasis, immune regulation, and tumor growth and development. Many reports have shown that miPs are especially essential for regulating glucose and lipid metabolism and regulating mitochondrial function.MiPs are also involved in the progression of related diseases. This paper reviews the sources and identification of miPs, as well as the functional significance of miPs for metabolism-related diseases, with the aim of revealing their potential clinical applications.
基金supported in part by the National Major Projects of National Committee of Sciences and Technology ，People’s Republic of China (No．96-9 16-03-07)；China Medical Board， New York(No．93-582)．
文摘OBJECTIVE: To investigate the genotypes of hepatitis E viruses (HEV) detected in sera of patients from different regions of China. METHODS: The partial genome (nt6461-6860, nt5994-6294) of open reading frame 2 (ORF2) of 45 HEV strains detected from 14 cities of China was amplified and sequenced using polymerase chain reaction (PCR) and direct sequencing. RESULTS: Forty-one of 45 strains (91%) share the same genotype with HEV Burma strain (B), with nucleotide identities higher than 98% with the representative HEV Chinese strain. Only 4 HEV strains are significantly divergent from the 3 prototype strains of HEV, with nucleotide identities of 77%-80% with HEV Burmese/Chinese strain, 74%-76% with Mexican strain and 74%-77% with the newly discovered HEV US/swine strain, respectively. Phylogenetic analysis suggests that these 4 strains may represent 2 different subtypes that belong to a novel genotype of HEV, which is significantly divergent from the prototype Mexico, Burmese and US/swine strains. CONCLUSION: Among patients with hepatitis E in China, most are infected by the Chinese prototype HEV, and only a small part by the new genotype HEV.
基金supported by the National Key R&D Program of China(Grant No.2016YFC0901702)National Natural Science Foundation of China(Grant Nos.81902519,91940306,31871294,31701117,and 31970647)+4 种基金the National Key R&D Program of China(Grant Nos.2017YFC0907503,2016YFC0901002,and 2018YFA0106901)the Strategic Priority Research Program of Chinese Academy of Sciences(Grant No.XDB38040300)the 13th Five-year Informatization Plan of Chinese Academy of Sciences(Grant No.XXH13505-05)Special Investigation on Science and Technology Basic Resources,Ministry of Science and Technology,China(Grant No.2019FY100102)the National Genomics Data Center,China。
文摘Small proteins specifically refer to proteins consisting of less than 100 amino acids translated from small open reading frames(s ORFs),which were usually missed in previous genome annotation.The significance of small proteins has been revealed in current years,along with the discovery of their diverse functions.However,systematic annotation of small proteins is still insufficient.Sm Prot was specially developed to provide valuable information on small proteins for scientific community.Here we present the update of Sm Prot,which emphasizes reliability of translated s ORFs,genetic variants in translated s ORFs,disease-specific s ORF translation events or sequences,and remarkably increased data volume.More components such as non-ATG translation initiation,function,and new sources are also included.Sm Prot incorporated638,958 unique small proteins curated from 3,165,229 primary records,which were computationally predicted from 419 ribosome profiling(Ribo-seq)datasets or collected from literature and other sources from 370 cell lines or tissues in 8 species(Homo sapiens,Mus musculus,Rattus norvegicus,Drosophila melanogaster,Danio rerio,Saccharomyces cerevisiae,Caenorhabditis elegans,and Escherichia coli).In addition,small protein families identified from human microbiomes were also collected.All datasets in Sm Prot are free to access,and available for browse,search,and bulk downloads at http://bigdata.ibp.ac.cn/SmProt/.
基金This work is supported by the National Natural Science Foundation of China(nos.31872872 and U1804113)National Key Research and Deveopment Program of China(no.2016YFD0101003),and Henan Association for Science and Technology.
文摘Non-conventional peptides(NCPs),which include small open reading frame-encoded peptides,play critical roles in fundamental biological processes.In this study,we developed an integrated peptidogenomic pipeline using high-throughput mass spectra to probe a customized six-frame translation database and applied it to large-scale identification of NCPs in plants.A total of 1993 and 1860 NCPs were unambiguously identified in maize and Arabidopsis,respectively.These NCPs showed distinct characteristics compared with conventional peptides and were derived from introns,3′UTRs,5′UTRs,junctions,and intergenic regions.Furthermore,our results showed that translation events in unannotated transcripts occur more broadly than previously thought.In addition,we found that dozens of maize NCPs are enriched within regions associated with phenotypic variations and domestication selection,indicating that they potentially are involved in genetic regulation of complex traits and domestication in maize.Taken together,our study developed an integrated peptidogenomic pipeline for large-scale identification of NCPs in plants,which would facilitate global characterization of NCPs from other plants.The identification of large-scale NCPs in both monocot(maize)and dicot(Arabidopsis)plants indicates that a large portion of plant genome can be translated into biologically functional molecules,which has important implications for functional genomic studies.
基金ThisstudywassupportedbytheNationalNaturalScienceFoundationofChina (No 3 9870 775 )
文摘Background DNA analysis has shown a lack of significant compatibility between couples affected by unexplained recurrent spontaneous abortion (URSA) compared with normal fertile couples, 8 although one study that made use of a PCR-sequence-specific oligonucleotide (SSO) method did observe evidence of significant compatibility in the HLA-DQA1 and DQB1 alleles between patients and aborted fetuses. 9 This study was designed to investigate whether URSA were associated with particular DQ alleles or promoter alleles.Methods Thirty-two patients with URSA and 54 women who had had at least one successful pregnancy were included in this study. HLA-DQ genotyping was performed by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The HLA-DQB1 promoter was detected by the SSO and sequence-specific primer (SSP) methods. The DQA1, DQB1, and DQB1 promoter (QBP) gene frequencies in the patients were compared with the gene frequencies in normal controls. The data were analyzed statistically with the χ 2 and Fisher’s exact tests.Results The results showed that the frequency of DQB1 *0604/0605 was significantly higher and the frequency of DQB1 *0501/0502 was significantly lower in the patient group as compared with the normal controls. In addition, the frequencies of the DQA1 *01-DQB1 *0604/0605 and QBP6.2-DQB1 *0604/0605 haplotypes were overrepresented in the patients relative to the controls. Our results did not show any differences between URSA patients and the controls with regard to DQA1 and QBP allele frequencies. Conclusions Our data suggest that URSA is associated with the HLA-DQB1 coding region, and is not associated with its upstream regulatory region. The DQB1 *0604/0605, DQA1 *01-DQB1 *0604/0605, and QBP6.2-DQB1 *0604/0605 haplotypes may confer susceptibility to URSA, while the DQB1 *0501/0502 allele may protect women from URSA.
基金funded in part by the Project from the Ministry of Science and Technology in China(2020YFC0841200)the National Major Science&Technology Project for Control and Prevention of Major Infectious Diseases in China(2017ZX10103004)+2 种基金the Chinese Academy of Medical Sciences(CAMS)Innovation Fund for Medical Sciences(2020HY320001)the non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences(2019PT310029)the Chinese Academy of Medical Sciences(CAMS)Innovation Fund for Medical Sciences(2016-I2M-1-014).
文摘The outbreak of coronavirus disease 2019(COVID-19)in Wuhan,China,was caused by a novel coronavirus(CoV),named severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).The rapid detection of viral nucleic acids is critical for the early identification of infected cases.We have developed two TaqMan real-time reverse transcription-PCR assays to detect SARS-CoV-2.The designed primers target the nucleocapsid(N)and open reading frame(ORF)1b gene regions,where the probes discriminate SARS-CoV-2 from other human and animal CoVs.The sensitivities are one genomic copy per reaction for theN gene assay and ten copies for the ORF 1b gene assay.The overall linear detection ranges are 1–10^(6)and 10–10^(6)copies per reaction for the N gene assay and the ORF 1b gene assay,respectively.Surveillance of 23 suspected COVID-19 patients demonstrated that SARS-CoV-2 could be detected from 100%(23/23)and 62.5%(16/23)of clinical specimens by the N gene assay and the ORF 1b gene assay,respectively.All of the samples not detected by the ORF 1b gene assay were throat swabs,indicating a lower viral load in the upper respiratory tract and the relatively lower sensitivity of the ORF 1b gene assay.The assays developed in the present study offer alternative diagnostic tests for COVID-19.
基金the National Natural Science Foundation of China(31970747 to X.S.,82050008 to B.L.).
文摘The GGGGCC(G_(4)C_(2))hexanucleotide repeat expansion in the C9ORF72 gene is a major cause of both hereditary amyotrophic lateral sclerosis and familial frontotemporal dementia.Recent studies have shown that G_(4)C_(2)hexanucleotide repeat-containing RNA transcripts((G_(4)C_(2))_(n)RNA)could go through liquid-liquid phase separation to form RNA foci,which may elicit neurodegeneration.However,the direct causality between these abnormal RNA foci and neuronal toxicity remains to be demonstrated.Here we introduce an optogenetic control system that can induce the assembly and phase separation of(G_(4)C_(2))_(n)RNA foci with blue light illumination in human cells,by fusing a specific(G_(4)C_(2))_(n)RNA binding protein as the linker domain to Cry2,a protein that oligomerizes in response to blue light.Our results demonstrate that a higher number of G_(4)C_(2)repeats have the potential to be induced into more RNA foci in the cells.Both spontaneous and induced RNA foci display liquid-like properties according to FRAP measurements.Computational simulation shows strong consistency with the experimental results and supports the effect of our system to promote the propensity of(G_(4)C_(2))_(n)RNA towards phase separation.This system can thus be used to investigate whether(G_(4)C_(2))_(n)RNA foci would disrupt normal cellular processes and lead to pathological phenotypes relevant to repeat expansion disorders.
