BACKGROUND Tenofovir alafenamide fumarate(TAF)is one of the first-line treatments used to treat chronic hepatitis B patients;TAF has strong antiviral activity and a high barrier to resistance.Although virological brea...BACKGROUND Tenofovir alafenamide fumarate(TAF)is one of the first-line treatments used to treat chronic hepatitis B patients;TAF has strong antiviral activity and a high barrier to resistance.Although virological breakthroughs in patients during TAF treatment are rare,patients with incomplete responses to TAF are occasionally observed.AIM To investigate responsible mutations in the reverse transcriptase region of hepatitis B virus(HBV)for TAF-incomplete responses.METHODS Thirteen chronic hepatitis B patients who received TAF monotherapy were included.A TAF-incomplete responder was defined as one who was continuously positive for HBV DNA over 2 years after TAF treatment initiation.The emergences of mutations in TAF-incomplete responders were evaluated before,one year after,and two years after treatment by deep sequencing of HBV DNA and RNA.RESULTS Two patients were continuously positive for HBV DNA over two years.The rtL269I mutation,one of the CYEI mutations linked to tenofovir resistance,was detected in both patients by direct sequencing.The deep sequencing analysis revealed that a combination of rtT118A and rtL220I mutations and the rtL269I mutation were predominantly detected in HBV DNA even when these mutations were barely detected in HBV RNA.This suggests a superior replication capability of the HBV variants with these mutations under TAF treatment.CONCLUSION The deep sequencing analysis of HBV DNA and RNA and comparing the detection rates of mutations were useful for estimating responsible mutations for TAF-incomplete responses.Such analysis is needed to evaluate the association between mutations that emerge during TAF treatment and incomplete responses to TAF.展开更多
Viral diseases are among the most critical damaging factors that impose a global threat to the cucurbit industry.China is the world’s leading country for the production and consumption of cucurbits.Guangdong,a provin...Viral diseases are among the most critical damaging factors that impose a global threat to the cucurbit industry.China is the world’s leading country for the production and consumption of cucurbits.Guangdong,a province in southern China dominated by the tropical and subtropical climate,favors the survival of different plant viruses and their vectors.Five main cucurbit crops showing various disease symptoms were surveyed and collected to identify viruses infecting cucurbits in Guangdong during 2018–2020.In the field,the incidence ranged from 5-30%,or even 60-100% in the case of severely infected cucurbits.A total of 357 symptomatic samples were collected and subsequently screened for cucurbit viruses by small RNA deep sequencing and assembly(sRSA).Seventeen virus species belonging to 10 genera were identified in the five main cucurbit crops.The most common viruses were papaya ringspot virus(PRSV;Potyvirus),zucchini tigre mosaic virus(ZTMV;Potyvirus),zucchini yellow mosaic virus(ZYMV;Potyvirus),and watermelon silver mottle virus(WSMoV;Orthotospovirus),with infection rates of 24.4,19.0,17.1,and 14.3%,respectively.Notably,the most prevalent viruses were melon yellow spot orthotospovirus(MYSV)in cucumber,PRSV in squash,cucumber green mottle mosaic virus(CGMMV;Tobamovirus)in bottle gourd,WSMoV in white gourd,and ZYMV in luffa.Mixed infections were prevalent,and the types of mixed infections varied substantially in different cucurbit crops.Moreover,the full-length nucleotide sequences of watermelon green mottle mosaic virus(WGMMV),CGMMV,and watermelon virus A(WVA;Wamavirus)identified in bottle gourd were cloned and analyzed.This study is the first reporting WGMMV infecting bottle gourd in China mainland.In summary,the results demonstrate that in Guangdong,the most prevalent viruses belong to potyviruses,orthotospoviruses,and tobamoviruses groups.The findings will facilitate agricultural researchers and farmers to plan and implement effective disease control strategies aiming at timely detection and management of cucurbit-infecting viral pathogens.展开更多
To identity the potential pathogen associated with the yellow vein clearing symptom on lemon trees, the profiles of virus-de- rived small interfering RNAs from citrus samples were obtained and analyzed by deep sequenc...To identity the potential pathogen associated with the yellow vein clearing symptom on lemon trees, the profiles of virus-de- rived small interfering RNAs from citrus samples were obtained and analyzed by deep sequencing method in this study. Twenty-seven contigs almost cover the full length genome of Citrus yellow vein clearing virus （CYVCV） isolate YN were obtained using the small RNA deep sequencing technology. Analysis showed that this isolate CQ shared the highest nucleotide identity with isolate Y1 （JX040635） and YN （KP313242）, both of which belong to the genus Mandarivirus in the family Alphaflexiviridae. Mapping analysis of viral-derived siRNA （vsiRNA） profiles revealed an uneven distribution pattern of their generations along both positive and negative genome strands, and 22- and 21-nt vsiRNAs ranked the majority. BLAST against viroids and other viral databases confirmed that this sample was single-infected only by CYVCV, which indicated that CYVCV was the exact causal agent for the yellow clearing symptom occurring on lemon. This is the first CYVCV isolate detected in Chongqing and the second in China. This result could provide a molecular basis for the investigation of citrus viral diseases to protect citrus health in this region.展开更多
Objective To investigate distinctive features in drug-resistant mutations （DRMs） and interpretations for reverse transcriptase inhibitors （RTIs） between proviral DNA and paired viral RNA in HIV-l-infected patients...Objective To investigate distinctive features in drug-resistant mutations （DRMs） and interpretations for reverse transcriptase inhibitors （RTIs） between proviral DNA and paired viral RNA in HIV-l-infected patients. Methods Forty-three HIV-l-infected individuals receiving first-line antiretroviral therapy were recruited to participate in a multicenter AIDS Cohort Study in Anhui and Henan Provinces in China in 2004. Drug resistance genotyping was performed by bulk sequencing and deep sequencing on the plasma and whole blood of 77 samples, respectively. Drug-resistance interpretation was compared between viral RNA and paired proviral DNA. Results Compared with bulk sequencing, deep sequencing could detect more DRMs and samples with DRMs in both viral RNA and proviral DNA. The mutations M1841 and M2301 were more prevalent in proviral DNA than in viral RNA （Fisher＇s exact test, P〈0.05）. Considering ＇majority resistant variants＇, 15 samples （19.48%） showed differences in drug resistance interpretation between viral RNA and proviral DNA, and 5 of these samples with different DRMs between proviral DNA and paired viral RNA showed a higher level of drug resistance to the first-line drugs. Considering ＇minority resistant variants＇, 22 samples （28.57%） were associated with a higher level of drug resistance to the tested RTIs for proviral DNA when compared with paired viral RNA. Conclusion Compared with viral RNA, the distinctive information of DRMs and drug resistance interpretations for proviral DNA could be obtained by deep sequencing, which could provide more detailed and precise information for drug resistance monitoring and the rational design of optimal antiretroviral therapy regimens.展开更多
MicroRNAs （miRNAs） are -21 nucleotide （nt）, endogenous RNAs that regulate gene expression in plants. Increasing evidence suggests that miRNAs play an important role in species-specific development in plants. Howev...MicroRNAs （miRNAs） are -21 nucleotide （nt）, endogenous RNAs that regulate gene expression in plants. Increasing evidence suggests that miRNAs play an important role in species-specific development in plants. However, the detailed miRNA profile divergence has not been performed among tomato species. In this study, the small RNA （sRNA） profiles of Solanum lycopersicum cultivar 9706 and Solanum habrochaites species PI 134417 were obtained by deep sequencing. Sixty-three known miRNA families were identified from these two species, of which 39 were common. Further miRNA profile comparison showed that 24 known non-conserved miRNA families were species-specific between these two tomato species. In addition, six conserved miRNA families displayed an apparent divergent expression pattern between the two tomato species. Our results suggested that species-specific, non-conserved miRNAs and divergent expression of conserved miRNAs might contribute to developmental changes and phenotypic variation between the two tomato species. Twenty new miRNAs were also identified in S. lycopersicum. This research significantly increases the number of known miRNA families in tomato and provides the first set of small RNAs in S. habrochaites. It also suggests that miRNAs have an important role in species-specific plant developmental regulation.展开更多
Malformations of cortical development(MCDs)represent one of the most common causes of childhood-onset epilepsy,and are often refractory to antiseizure medications(Guerrini,2006;Guerrini and Dobyns,2014;Severino et al....Malformations of cortical development(MCDs)represent one of the most common causes of childhood-onset epilepsy,and are often refractory to antiseizure medications(Guerrini,2006;Guerrini and Dobyns,2014;Severino et al.,2020).Mild malformation of cortical development with oligodendroglial hyperplasia in epilepsy(MOGHE)is a newly recognized subtype of Focal Cortical Dysplasia(FCD),which was officially added to the FCD classification in 2022 by the International League Against Epilepsy(ILAE)(Najm et al.,2022).展开更多
In this review,the advantages and advances in applying high-throughput sequencing(HTS)in the management of viral diseases in citrus,along with some challenges,are discussed to provide perspectives on future prospects....In this review,the advantages and advances in applying high-throughput sequencing(HTS)in the management of viral diseases in citrus,along with some challenges,are discussed to provide perspectives on future prospects.Since the initial implementation of HTS in citrus virology,a substantial number of citrus viruses have been identified,with a notable increase in the last 7 years.The acquisition of viral genomes and various HTS-based omics analyses serve as crucial pillars for advancing research in the etiology,epidemiology,pathology,evolution,ecology,and biotechnology of citrus viruses.HTS has notably contributed to disease diagnosis,such as the diagnoses of concave gum and impietratura,as well as to the surveillance of new virus risks and the preparation of virus-free materials.However,certain inherent defects in HTS and coupled bioinformatics analysis,such as challenges with sequence assembly and the detection of viral dark matter,require improvement to enhance practical efficiency.In addition,the utilization of HTS for the systematic management of citrus viral diseases remains limited,and drawing insights from other virus-plant pathosystems while integrating emerging compatible techniques and ideas may broaden its specific applications.展开更多
In plants, non-coding small RNAs play a vital role in plant development and stress responses. To explore the possible role of non-coding small RNAs in the regulation of the jasmonate （JA） pathway, we compared the no...In plants, non-coding small RNAs play a vital role in plant development and stress responses. To explore the possible role of non-coding small RNAs in the regulation of the jasmonate （JA） pathway, we compared the non-coding small RNAs between the JA-deficient aos mutant and the JA-treated wild type Arabidopsis via high-throughput sequencing. Thirty new miRNAs and 27 new miRNA candidates were identified through bioinformatics approach. Forty-nine known miRNAs （belonging to 24 families）, 15 new miRNAs and new miRNA candidates （belonging to 11 families） and 3 tasiRNA families were induced by JA, whereas 1 new miRNA, 1 tasiRNA family and 22 known miRNAs （belonging to 9 families） were repressed by JA.展开更多
The importance of zinc （Zn） as a micronutrient essential for plant growth and development is becoming increasingly apparent. Much of the world’s soil is Zn-deficient, and soil-based Zn deficiency is often accompani...The importance of zinc （Zn） as a micronutrient essential for plant growth and development is becoming increasingly apparent. Much of the world’s soil is Zn-deficient, and soil-based Zn deficiency is often accompanied by Zn deficiency in human populations. MicroRNAs （miRNAs） play important roles in the regulation of plant gene expression at the level of translation. Many miRNAs involved in the modulation of heavy metal toxicity responses in plants have been identiifed;however, the role of miRNAs in the plant Zn deifciency response is almost completely unknown. Using high-throughput Solexa sequencing, we identiifed several miRNAs that respond to Zn deifciency in Brassica juncea roots. At least 21 conserved candidate miRNA families, and 101 individual members within those families, were identiifed in both the control and the Zn-deifcient B. juncea roots. Among this, 15 miRNAs from 9 miRNA families were differentially expressed in the control and Zn-deifcient plants. Of the 15 differentially expressed miRNAs, 13 were up-regulated in the Zn-deifcient B. juncea roots, and only two, miR399b and miR845a, were down-regulated. Bioinformatics analysis indicated that these miRNAs were involved in modulating phytohormone response, plant growth and development, and abiotic stress responses in B. juncea roots. These data help to lay the foundation for further understanding of miRNA function in the regulation of the plant Zn deifciency response and its impact on plant growth and development.展开更多
The plant genome possesses a large number of microRNAs （miRNAs） mainly 21-24 nucleotides in length. They play a vital role in regulation of target gene expression at various stages throughout the whole plant life cy...The plant genome possesses a large number of microRNAs （miRNAs） mainly 21-24 nucleotides in length. They play a vital role in regulation of target gene expression at various stages throughout the whole plant life cycle. Here we sequenced and analyzed ~ 10 million non-coding RNAs （ncRNAs） derived from fiber tissue of the allotetraploid cotton （Gossypium hirsutum） 7 days post-anthesis using ncRNA-seq technology. In terms of distinct reads, 24 nt ncRNA is by far the dominant species, followed by 21 nt and 23 nt ncRNAs. Using ab initio prediction, we identified and characterized a total of 562 candidate miRNA gene loci on the recently assembled D5 genome of the diploid cotton G. raimondii. Of all the 562 predicted miRNAs, 22 were previously discovered in cotton species and 187 had sequence conservation and homology to homologous miRNAs of other plant species. Nucleotide bias analysis showed that the 9th and 1st positions were significantly conserved among different types of miRNA genes. Among the 463 putative miRNA target genes, most significant up/down-regulation occurred in 10-20 days post-anthesis, indicating that miRNAs played an important role during the elongation and secondary cell wall synthesis stages of cotton fiber development. The discovery of new miRNA genes will help understand the mechanisms of miRNA generation and regulation in cotton.展开更多
Two traditional Chinese medicines(TCMs),namely WangshiBaochiwan and Panax Notoginseng Saponins(notoginsenoside),were chosen to study their effects on gut microbiota.Both of them have a long history of application in C...Two traditional Chinese medicines(TCMs),namely WangshiBaochiwan and Panax Notoginseng Saponins(notoginsenoside),were chosen to study their effects on gut microbiota.Both of them have a long history of application in China.During a test of 28 d,different doses of the medicines were administered to male Wistar rats daily.At the end of the administration,fresh fecal samples were collected and subjected to 16S rRNA sequencing to determine the profiles of gut microbiota.In relative to the controls,effects on gut microbiota were evaluated with medicine-treated rats.Consistent with its unique bidirectional effects on constipation and diarrhea,treatment of WangshiBaochiwan led to a balanced regulation of Lactobacillus and Bacteroides.The treatment also led to increased populations of Ruminiclostridium_9 and Eubacterium_ventriosum that are the major producer of short-chain fatty acid(SCFA),and decreased populations of genus Jeotgalicoccus and Bilophila that are associated with inflammation.These changes therefore resulted in a much healthier microbiota environment in WangshiBaochiwan-treated rates.For the treatment of notoginsenoside,effects were found with Enterobacteriaceae species that is associated with Parkinson's disease,Christensenellaceae family that is associated with aging,and hypertension-associated Rikenellaceae,Christensenellaceae,Lachnospiraceae and Bacteroidaceae species.In agreement with its major indications,the treatment further led to increased populations of SCFA-producing bacteria,such as Elusimicrobium,Anaerotruncus,Ruminococcaceae_NK4A214_group,and Intestinimonas.Taken together,treatment of the two TCMs led to active and distinguishable regulations of gut microbiota.Impressively,these changes were in agreement with their clinical efficacy,and suggested that they were involved in the treatment of these diseases.展开更多
Peripheral nerve injury may trigger changes in mRNA levels in the spinal cord.Finding key mRNAs is important for improving repair after nerve injury.This study aimed to investigate changes in mRNAs in the spinal cord ...Peripheral nerve injury may trigger changes in mRNA levels in the spinal cord.Finding key mRNAs is important for improving repair after nerve injury.This study aimed to investigate changes in mRNAs in the spinal cord following sciatic nerve injury by transcriptomic analysis.The left sciatic nerve denervation model was established in C57 BL/6 mice.The left L4–6 spinal cord segment was obtained at 0,1,2,4 and 8 weeks after severing the sciatic nerve.mRNA expression profiles were generated by RNA sequencing.The sequencing results of spinal cord mRNA at 1,2,4,and 8 weeks after severing the sciatic nerve were compared with those at 0 weeks by bioinformatic analysis.We identified 1915 differentially expressed mRNAs in the spinal cord,of which 4,1909,and 2 were differentially expressed at 1,4,and 8 weeks after sciatic nerve injury,respectively.Sequencing results indicated that the number of differentially expressed mRNAs in the spinal cord was highest at 4 weeks after sciatic nerve injury.These mRNAs were associated with the cellular response to lipid,ATP metabolism,energy coupled proton transmembrane transport,nuclear transcription factor complex,vacuolar proton-transporting V-type ATPase complex,inner mitochondrial membrane protein complex,tau protein binding,NADH dehydrogenase activity and hydrogen ion transmembrane transporter activity.Of these mRNAs,Sgk1,Neurturin and Gpnmb took part in cell growth and development.Pathway analysis showed that these mRNAs were mainly involved in aldosterone-regulated sodium reabsorption,oxidative phosphorylation and collecting duct acid secretion.Functional assessment indicated that these mRNAs were associated with inflammation and cell morphology development.Our findings show that the number and type of spinal cord mRNAs involved in changes at different time points after peripheral nerve injury were different.The number of differentially expressed mRNAs in the spinal cord was highest at 4 weeks after sciatic nerve injury.These results provide reference data for finding new targets for the treatment of peripheral nerve injury,and for further gene therapy studies of peripheral nerve injury and repair.The study procedures were approved by the Ethics Committee of the Peking University People's Hospital(approval No.2017 PHC004)on March 5,2017.展开更多
Wang Shi Bao Chi Wan(WSBCW)is a traditional Chinese medicine with a recorded administration history of more than 180 years.In the present study,the preclinical safety of WSBCW was evaluated the preclinical safety of W...Wang Shi Bao Chi Wan(WSBCW)is a traditional Chinese medicine with a recorded administration history of more than 180 years.In the present study,the preclinical safety of WSBCW was evaluated the preclinical safety of WSBCW using a toxicity test,which consisted of an administration period of 28 d and a recovery period of 15 d.During the test,male and female SD rats were administered the medicine once a day by oral gavage,at a dose of 60 mg/kg/day,600 mg/kg/day,or 1500 mg/kg/day.As a reference medicine,mosapride citrate was administered at a dose of 37.5 mg/kg/day,which was clinically equivalent to the high-dosage treatment of WSBCW.With all the dosage groups,statistically,no adverse effect was observed in terms of clinical observation,food intake,body weights,organ coefficient,blood biochemistry,and histopathology examination.No intestinal melanosis was observed in the rats.When the data were examined animal by animal,test substance-related adverse effects were found with the high-dosage rats in hematology assay.The deranged,however,reversible changes suggested a compromised intestinal barrier,which was also observed with in mosapride citrate-treated rats.In addition to the histopathology assay,molecular toxicology was explored using high-throughput gene sequencing.No evident toxicity was revealed.In summary,administration of WSBCW was well tolerated within a treatment of 28 d.展开更多
Rice stripe virus（RSV） often causes severe rice yield loss in temperate regions of East Asia. Although the correlation of small interfering RNAs（si RNAs） with transgenic virus resistance of plants using RNA interf...Rice stripe virus（RSV） often causes severe rice yield loss in temperate regions of East Asia. Although the correlation of small interfering RNAs（si RNAs） with transgenic virus resistance of plants using RNA interference（RNAi） is known for decades, no systematical research has been done on the profiling of si RNAs from a genomic scale. Our research is aiming to systematically study the RNAi impact in RSV-resistant transgenic rice, which was generated by introducing an inverted repeat construct that targets RSV nucleocapsid protein（NCP） gene. In this paper, three independent RSV-retsistant transgenic rice lines were generated, their stable integration of the T-DNA fragment and the expression of si RNAs were confirmed by Southern blotting and Northern blotting analyses, and the majority of si RNAs were in lengths of 21, 22, and 24 nucleotides（nt）, which have validated a connection between the presence of the RSV NCP homologous si RNAs and the RSV resistance in those transgenic rice lines. In one of these transgenic lines（T4-B1）, the T-DNA fragment was found to have been inserted at chromosome 1 of the rice genome, substituting the rice genome fragment from 32 158 773 to 32 158 787 nt. Bioinformatics analysis of small RNA-Seq data on the T4-B1 line also confirmed the large population of NCP-derived si RNAs in transgenic plants, and the RSV-infected library（T4-B1-V） possessed more si RNAs than its mock inoculated libraries（T4-B1-VF）, these results indicating the inverted repeat construct and RSV could introduce abundance of si RNAs in transgenic rice. Moreover, a varied expression level of specific si RNAs was found among different segments of the NCP gene template, about 47% of NCP-derived si RNAs reads aligned with the fragment from 594 to 832 nt（239 nt in length） in NCP gene（969 nt in length） in the T4-B1-V, indicating a potential usage of hotspot regions for RNAi silencing in future research. In conclusion, as the first study to address the si RNA profile in RSV-resistant transgenic plant using next generation sequencing（NGS） technique, we confirmed that the massive abundance of si RNA derived from the inverted repeat of NCP is the major reason for RSV-resistance.展开更多
Two microRNA （miRNA） quantification methods, namely, poly（A） reverse transcription （RT）-quantitative real-time polymerase chain reaction （qPCR） and stem-loop RT-qPCR, have been developed for quantifying miRNA ...Two microRNA （miRNA） quantification methods, namely, poly（A） reverse transcription （RT）-quantitative real-time polymerase chain reaction （qPCR） and stem-loop RT-qPCR, have been developed for quantifying miRNA expression. In the present study, five miRNAs, including miR166, miR167, miR168, miR159, and miR396, with different sequence frequencies, were selected as targets to compare their expression profiles in five wheat tissues by applying the two methods and deep sequencing. The study aimed to determine a simple, reliable and high-throughput method for detecting miRNA expressions in wheat tissues. Results showed that the miRNA expression profiles determined by poly（A） RT-qPCR were more consistent with those obtained by deep sequencing. Further analysis indicated that the correlation coefficients of the data obtained by poly（A） RT-qPCR and deep sequencing （0.739, P≤0.01） were higher than those obtained by stem-loop RT-qPCR and deep sequencing （0.535, P≤0.01）. The protocol used for poly（A） RT-qPCR is simpler than that for stem-loop RT-qPCR. Thus, poly（A） RT-qPCR was a more suitable high-throughput assay for detecting miRNA expression profiles. To the best of our knowledge, this study was the first to compare these two miRNA quantification methods. We also provided useful information for quantifying miRNA in wheat or other plant species.展开更多
With the accomplishment of the genome draft sequences, identification of functional elements in genome has become an urgent task. Full-length cDNAs provide an important resource for gene identification and their preci...With the accomplishment of the genome draft sequences, identification of functional elements in genome has become an urgent task. Full-length cDNAs provide an important resource for gene identification and their precise structural feature determination. It also provides a basis for genomic element definition. As many regulatory elements are around transcription start sites(TSSs), precise localization of TSSs in the genome becomes a critical step for identifying the associated core promoters. Massive parallel snapshot of TSSs at a particular time under a specific experimental condition makes it possible to globally analyze important regulatory elements around TSSs and further construct transcriptional regulatory networks. In this paper, we first reviewed two important full-length cDNA cloning techniques: cap-trapper technique and oligo-capping technique. Then,we introduced deepCAGE, a cap-trapper and deep sequencing-based TSS profiling technique, and its applications in the research of transcriptional regulation.展开更多
This is the first systematic investigation of viral pathogens in <i>Vitis</i> <i>vinifera</i> from Hangzhou vicinity of China. About 7 viruses and 5 viroids were annotated from four production ...This is the first systematic investigation of viral pathogens in <i>Vitis</i> <i>vinifera</i> from Hangzhou vicinity of China. About 7 viruses and 5 viroids were annotated from four production bases “Dushicun”, “Wangjiayuan”, “Xiajiangcun”, and “Yangducun” covering 15 cultivars through sRNAseq technique. At least 3 viruses<a name="OLE_LINK4"></a>—grapevine leaf roll-associated virus 3 (GLRaV-3), grapevine fleck <span>virus (GFkV) and grapevine geminivirus A (GGVA), and 4 viroids—hop stunt</span> viroid (HSVd), citrus viroid II (CVd-II), grapevine yellow speckle viroid 1 (GYSVd-1) and grapevine yellow speckle viroid 2 (GYSVd-2) infected all four bases. “Yangducun” base showed 11, the most infected pathogens. GYSVd-1 showed the highest accumulation in host of Wangjiayuan base. The main in<span>fected pathogens were verified by reverse-transcription polymerase chain reaction</span> (RT-PCR) technique, the detected rate reached to 85% - 100%. The results provide an important basis for effective and precise detection of viral diseases in the area and for the virus-free cultivation in future.展开更多
The human retina serves as a light detector and signals transmission tissue.Advanced insights into retinal disease mechanisms and therapeutic strategies require a deep understanding of healthy retina molecular events....The human retina serves as a light detector and signals transmission tissue.Advanced insights into retinal disease mechanisms and therapeutic strategies require a deep understanding of healthy retina molecular events.Here,we sequenced the m RNA of over 0.6 million single cells from human retinas across six regions at nine different ages.Sixty cell sub-types have been identified from the human mature retinas with unique markers.We revealed regional and age differences of gene expression profiles within the human retina.Cell-cell interaction analysis indicated a rich synaptic connection within the retinal cells.Gene expression regulon analysis revealed the specific expression of transcription factors and their regulated genes in human retina cell types.Some of the gene’s expression,such as DKK3,are elevated in aged retinas.A further functional investigation suggested that over expression of DKK3 could impact mitochondrial stability.Overall,decoding the molecular dynamic architecture of the human retina improves our understanding of the vision system.展开更多
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 eval...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.展开更多
We assembled a total of 297,239 Gossypium hirsutum （Gh, a tetraploid cotton, AADD） expressed sequence tag （EST） sequences that were available in the National Center for Biotechnology Information database, with ref...We assembled a total of 297,239 Gossypium hirsutum （Gh, a tetraploid cotton, AADD） expressed sequence tag （EST） sequences that were available in the National Center for Biotechnology Information database, with reference to the recently published G. raimondii （Gr, a diploid cotton, DD） genome, and obtained 49,125 UniGenes. The average lengths of the U niGenes were increased from 804 and 791 bp in two previous EST assemblies to 1,019 bp in the current analysis. The number of putative cotton UniGenes with lengths of 3 kb or more increased from 25 or 34 to 1,223. As a result, thousands of originally independent G. hirsutum ESTs were aligned to produce large contigs encoding transcripts with very long open reading frames, indicating that the G. raimondii genome sequence provided remarkable advantages to assemble the tetraploid cotton transcriptome. Significant different distribution patterns within several GO terms, including transcription factor activity, were observed between D- and A-derived assemblies. Tran- scriptome analysis showed that, in a tetraploid cotton cell, 29,547 UniGenes were possibly derived from the D subgenome while another 19,578 may come from the A subgenome. Finally, some of the in silico data were confirmed by reverse transcription polymerase chain reaction experiments to show the changes in transcript levels for several gene families known to play key role in cotton fiber development. We believe that our work provides a useful platform for functional and evolutionary genomic studies in cotton.展开更多
基金Supported by the Japan Agency for Medical Research and Development(AMED),No.JP22fk0310503.
文摘BACKGROUND Tenofovir alafenamide fumarate(TAF)is one of the first-line treatments used to treat chronic hepatitis B patients;TAF has strong antiviral activity and a high barrier to resistance.Although virological breakthroughs in patients during TAF treatment are rare,patients with incomplete responses to TAF are occasionally observed.AIM To investigate responsible mutations in the reverse transcriptase region of hepatitis B virus(HBV)for TAF-incomplete responses.METHODS Thirteen chronic hepatitis B patients who received TAF monotherapy were included.A TAF-incomplete responder was defined as one who was continuously positive for HBV DNA over 2 years after TAF treatment initiation.The emergences of mutations in TAF-incomplete responders were evaluated before,one year after,and two years after treatment by deep sequencing of HBV DNA and RNA.RESULTS Two patients were continuously positive for HBV DNA over two years.The rtL269I mutation,one of the CYEI mutations linked to tenofovir resistance,was detected in both patients by direct sequencing.The deep sequencing analysis revealed that a combination of rtT118A and rtL220I mutations and the rtL269I mutation were predominantly detected in HBV DNA even when these mutations were barely detected in HBV RNA.This suggests a superior replication capability of the HBV variants with these mutations under TAF treatment.CONCLUSION The deep sequencing analysis of HBV DNA and RNA and comparing the detection rates of mutations were useful for estimating responsible mutations for TAF-incomplete responses.Such analysis is needed to evaluate the association between mutations that emerge during TAF treatment and incomplete responses to TAF.
基金supported by the grants from the National Natural Science Foundation of China(31801712)the Key Research and Development Program of Guangdong Province,China(2018B020202006)+1 种基金the Agricultural Competitive Industry Discipline Team Building Project of Guangdong Academy of Agricultural Sciences(202103TD and 202105TD)the Development Program for Guangdong Province Modern Agricultural Science and Technology Innovation Alliance(2020KJ113)。
文摘Viral diseases are among the most critical damaging factors that impose a global threat to the cucurbit industry.China is the world’s leading country for the production and consumption of cucurbits.Guangdong,a province in southern China dominated by the tropical and subtropical climate,favors the survival of different plant viruses and their vectors.Five main cucurbit crops showing various disease symptoms were surveyed and collected to identify viruses infecting cucurbits in Guangdong during 2018–2020.In the field,the incidence ranged from 5-30%,or even 60-100% in the case of severely infected cucurbits.A total of 357 symptomatic samples were collected and subsequently screened for cucurbit viruses by small RNA deep sequencing and assembly(sRSA).Seventeen virus species belonging to 10 genera were identified in the five main cucurbit crops.The most common viruses were papaya ringspot virus(PRSV;Potyvirus),zucchini tigre mosaic virus(ZTMV;Potyvirus),zucchini yellow mosaic virus(ZYMV;Potyvirus),and watermelon silver mottle virus(WSMoV;Orthotospovirus),with infection rates of 24.4,19.0,17.1,and 14.3%,respectively.Notably,the most prevalent viruses were melon yellow spot orthotospovirus(MYSV)in cucumber,PRSV in squash,cucumber green mottle mosaic virus(CGMMV;Tobamovirus)in bottle gourd,WSMoV in white gourd,and ZYMV in luffa.Mixed infections were prevalent,and the types of mixed infections varied substantially in different cucurbit crops.Moreover,the full-length nucleotide sequences of watermelon green mottle mosaic virus(WGMMV),CGMMV,and watermelon virus A(WVA;Wamavirus)identified in bottle gourd were cloned and analyzed.This study is the first reporting WGMMV infecting bottle gourd in China mainland.In summary,the results demonstrate that in Guangdong,the most prevalent viruses belong to potyviruses,orthotospoviruses,and tobamoviruses groups.The findings will facilitate agricultural researchers and farmers to plan and implement effective disease control strategies aiming at timely detection and management of cucurbit-infecting viral pathogens.
基金supported by the National Natural Science Foundation of China(31501611)the Special Fund for Agro-scientific Research in the Public Interest,China (201203076)the Fundamental Research Funds for the Central Universities,China(XDJK2016B021,SWU116012,XDJK2014A001 and XDJK2015A009)
文摘To identity the potential pathogen associated with the yellow vein clearing symptom on lemon trees, the profiles of virus-de- rived small interfering RNAs from citrus samples were obtained and analyzed by deep sequencing method in this study. Twenty-seven contigs almost cover the full length genome of Citrus yellow vein clearing virus （CYVCV） isolate YN were obtained using the small RNA deep sequencing technology. Analysis showed that this isolate CQ shared the highest nucleotide identity with isolate Y1 （JX040635） and YN （KP313242）, both of which belong to the genus Mandarivirus in the family Alphaflexiviridae. Mapping analysis of viral-derived siRNA （vsiRNA） profiles revealed an uneven distribution pattern of their generations along both positive and negative genome strands, and 22- and 21-nt vsiRNAs ranked the majority. BLAST against viroids and other viral databases confirmed that this sample was single-infected only by CYVCV, which indicated that CYVCV was the exact causal agent for the yellow clearing symptom occurring on lemon. This is the first CYVCV isolate detected in Chongqing and the second in China. This result could provide a molecular basis for the investigation of citrus viral diseases to protect citrus health in this region.
基金supported by grants from the State Key Laboratory of Infectious Disease Prevention and Control(2011SKLID102)the National Nature Science Foundation of China(81172733 and 81561128006)the 12th Five-Year National Science and Technology Major Project(2013ZX10001-006)
文摘Objective To investigate distinctive features in drug-resistant mutations （DRMs） and interpretations for reverse transcriptase inhibitors （RTIs） between proviral DNA and paired viral RNA in HIV-l-infected patients. Methods Forty-three HIV-l-infected individuals receiving first-line antiretroviral therapy were recruited to participate in a multicenter AIDS Cohort Study in Anhui and Henan Provinces in China in 2004. Drug resistance genotyping was performed by bulk sequencing and deep sequencing on the plasma and whole blood of 77 samples, respectively. Drug-resistance interpretation was compared between viral RNA and paired proviral DNA. Results Compared with bulk sequencing, deep sequencing could detect more DRMs and samples with DRMs in both viral RNA and proviral DNA. The mutations M1841 and M2301 were more prevalent in proviral DNA than in viral RNA （Fisher＇s exact test, P〈0.05）. Considering ＇majority resistant variants＇, 15 samples （19.48%） showed differences in drug resistance interpretation between viral RNA and proviral DNA, and 5 of these samples with different DRMs between proviral DNA and paired viral RNA showed a higher level of drug resistance to the first-line drugs. Considering ＇minority resistant variants＇, 22 samples （28.57%） were associated with a higher level of drug resistance to the tested RTIs for proviral DNA when compared with paired viral RNA. Conclusion Compared with viral RNA, the distinctive information of DRMs and drug resistance interpretations for proviral DNA could be obtained by deep sequencing, which could provide more detailed and precise information for drug resistance monitoring and the rational design of optimal antiretroviral therapy regimens.
基金supported by the National Basic Research Program of China (2009CB11900)the Special Fund for Agro-Scientific Research in the Public Interest, China (201003065)
文摘MicroRNAs （miRNAs） are -21 nucleotide （nt）, endogenous RNAs that regulate gene expression in plants. Increasing evidence suggests that miRNAs play an important role in species-specific development in plants. However, the detailed miRNA profile divergence has not been performed among tomato species. In this study, the small RNA （sRNA） profiles of Solanum lycopersicum cultivar 9706 and Solanum habrochaites species PI 134417 were obtained by deep sequencing. Sixty-three known miRNA families were identified from these two species, of which 39 were common. Further miRNA profile comparison showed that 24 known non-conserved miRNA families were species-specific between these two tomato species. In addition, six conserved miRNA families displayed an apparent divergent expression pattern between the two tomato species. Our results suggested that species-specific, non-conserved miRNAs and divergent expression of conserved miRNAs might contribute to developmental changes and phenotypic variation between the two tomato species. Twenty new miRNAs were also identified in S. lycopersicum. This research significantly increases the number of known miRNA families in tomato and provides the first set of small RNAs in S. habrochaites. It also suggests that miRNAs have an important role in species-specific plant developmental regulation.
基金support from the following grants:the Natural Science Foundation of Beijing Municipality(7242149,L202034,7244416)the E-Town Cooperation&Development Foundation(YCXJ-JZ-2023-017)+3 种基金the National Natural Science Foundation of China(82171694,81901155)National High Level Hospital Clinical Research Funding(High Quality Clinical Research Project of Peking University First Hospital)(23cz020202)National High Level Hospital Clinical Research Funding(Youth Clinical Research Project of Peking University First Hospital)(2023YC19)National High Level Hospital Clinical Research Funding(Scientific Research Seed Fund of Peking University First Hospital)(2023SF42).
文摘Malformations of cortical development(MCDs)represent one of the most common causes of childhood-onset epilepsy,and are often refractory to antiseizure medications(Guerrini,2006;Guerrini and Dobyns,2014;Severino et al.,2020).Mild malformation of cortical development with oligodendroglial hyperplasia in epilepsy(MOGHE)is a newly recognized subtype of Focal Cortical Dysplasia(FCD),which was officially added to the FCD classification in 2022 by the International League Against Epilepsy(ILAE)(Najm et al.,2022).
基金supported by National Natural Science Foundation of China(Grant Nos.32370005,32072389)Chongqing Science Funds for Distinguished Young Scientists(Grant No.CSTB2022NSCQ-JQX0027)+3 种基金Innovation Research 2035 Pilot Plan of Southwest University(Grant Nos.SWU-XDPY22002,SWUXDZD22002)Special Fund for Youth Team of Southwest University(Grant No.SWU-XJLJ202310)Chongqing Talents of Exceptional Young Talents Project(Grant No.cstc2022ycjh-bgzxm0143)Chongqing Municipal Training Program of Innovation and Entrepreneurship for Undergraduates(Grant No.S202310635160)。
文摘In this review,the advantages and advances in applying high-throughput sequencing(HTS)in the management of viral diseases in citrus,along with some challenges,are discussed to provide perspectives on future prospects.Since the initial implementation of HTS in citrus virology,a substantial number of citrus viruses have been identified,with a notable increase in the last 7 years.The acquisition of viral genomes and various HTS-based omics analyses serve as crucial pillars for advancing research in the etiology,epidemiology,pathology,evolution,ecology,and biotechnology of citrus viruses.HTS has notably contributed to disease diagnosis,such as the diagnoses of concave gum and impietratura,as well as to the surveillance of new virus risks and the preparation of virus-free materials.However,certain inherent defects in HTS and coupled bioinformatics analysis,such as challenges with sequence assembly and the detection of viral dark matter,require improvement to enhance practical efficiency.In addition,the utilization of HTS for the systematic management of citrus viral diseases remains limited,and drawing insights from other virus-plant pathosystems while integrating emerging compatible techniques and ideas may broaden its specific applications.
基金supported by grants from the National Basic Research 973 Program (2011CB915404)the National Natural Science Foundation of China (91017012)the National Program of Transgenic Variety Development of China (2011ZX08009-004)
文摘In plants, non-coding small RNAs play a vital role in plant development and stress responses. To explore the possible role of non-coding small RNAs in the regulation of the jasmonate （JA） pathway, we compared the non-coding small RNAs between the JA-deficient aos mutant and the JA-treated wild type Arabidopsis via high-throughput sequencing. Thirty new miRNAs and 27 new miRNA candidates were identified through bioinformatics approach. Forty-nine known miRNAs （belonging to 24 families）, 15 new miRNAs and new miRNA candidates （belonging to 11 families） and 3 tasiRNA families were induced by JA, whereas 1 new miRNA, 1 tasiRNA family and 22 known miRNAs （belonging to 9 families） were repressed by JA.
基金supported by the Knowledge Innovation Program of the Chinese Academy of Sciences(KSCX2EW-Q-25)the National Natural Sciences Foundation of China(31170228+4 种基金31272239)the Key Project of State Key Laboratory of Desert and Oasis EcologyXinjiang Institute of Ecology and Geography of Chinese Academy of SciencesHebei Province Natural Sciences Foundation for Distinguished Young ScientistsChina (C2013503042)
文摘The importance of zinc （Zn） as a micronutrient essential for plant growth and development is becoming increasingly apparent. Much of the world’s soil is Zn-deficient, and soil-based Zn deficiency is often accompanied by Zn deficiency in human populations. MicroRNAs （miRNAs） play important roles in the regulation of plant gene expression at the level of translation. Many miRNAs involved in the modulation of heavy metal toxicity responses in plants have been identiifed;however, the role of miRNAs in the plant Zn deifciency response is almost completely unknown. Using high-throughput Solexa sequencing, we identiifed several miRNAs that respond to Zn deifciency in Brassica juncea roots. At least 21 conserved candidate miRNA families, and 101 individual members within those families, were identiifed in both the control and the Zn-deifcient B. juncea roots. Among this, 15 miRNAs from 9 miRNA families were differentially expressed in the control and Zn-deifcient plants. Of the 15 differentially expressed miRNAs, 13 were up-regulated in the Zn-deifcient B. juncea roots, and only two, miR399b and miR845a, were down-regulated. Bioinformatics analysis indicated that these miRNAs were involved in modulating phytohormone response, plant growth and development, and abiotic stress responses in B. juncea roots. These data help to lay the foundation for further understanding of miRNA function in the regulation of the plant Zn deifciency response and its impact on plant growth and development.
文摘The plant genome possesses a large number of microRNAs （miRNAs） mainly 21-24 nucleotides in length. They play a vital role in regulation of target gene expression at various stages throughout the whole plant life cycle. Here we sequenced and analyzed ~ 10 million non-coding RNAs （ncRNAs） derived from fiber tissue of the allotetraploid cotton （Gossypium hirsutum） 7 days post-anthesis using ncRNA-seq technology. In terms of distinct reads, 24 nt ncRNA is by far the dominant species, followed by 21 nt and 23 nt ncRNAs. Using ab initio prediction, we identified and characterized a total of 562 candidate miRNA gene loci on the recently assembled D5 genome of the diploid cotton G. raimondii. Of all the 562 predicted miRNAs, 22 were previously discovered in cotton species and 187 had sequence conservation and homology to homologous miRNAs of other plant species. Nucleotide bias analysis showed that the 9th and 1st positions were significantly conserved among different types of miRNA genes. Among the 463 putative miRNA target genes, most significant up/down-regulation occurred in 10-20 days post-anthesis, indicating that miRNAs played an important role during the elongation and secondary cell wall synthesis stages of cotton fiber development. The discovery of new miRNA genes will help understand the mechanisms of miRNA generation and regulation in cotton.
基金The National Natural Science Foundation of China(Grant No.31571403)Beijing Natural Science Foundation(Grant No.2171001).
文摘Two traditional Chinese medicines(TCMs),namely WangshiBaochiwan and Panax Notoginseng Saponins(notoginsenoside),were chosen to study their effects on gut microbiota.Both of them have a long history of application in China.During a test of 28 d,different doses of the medicines were administered to male Wistar rats daily.At the end of the administration,fresh fecal samples were collected and subjected to 16S rRNA sequencing to determine the profiles of gut microbiota.In relative to the controls,effects on gut microbiota were evaluated with medicine-treated rats.Consistent with its unique bidirectional effects on constipation and diarrhea,treatment of WangshiBaochiwan led to a balanced regulation of Lactobacillus and Bacteroides.The treatment also led to increased populations of Ruminiclostridium_9 and Eubacterium_ventriosum that are the major producer of short-chain fatty acid(SCFA),and decreased populations of genus Jeotgalicoccus and Bilophila that are associated with inflammation.These changes therefore resulted in a much healthier microbiota environment in WangshiBaochiwan-treated rates.For the treatment of notoginsenoside,effects were found with Enterobacteriaceae species that is associated with Parkinson's disease,Christensenellaceae family that is associated with aging,and hypertension-associated Rikenellaceae,Christensenellaceae,Lachnospiraceae and Bacteroidaceae species.In agreement with its major indications,the treatment further led to increased populations of SCFA-producing bacteria,such as Elusimicrobium,Anaerotruncus,Ruminococcaceae_NK4A214_group,and Intestinimonas.Taken together,treatment of the two TCMs led to active and distinguishable regulations of gut microbiota.Impressively,these changes were in agreement with their clinical efficacy,and suggested that they were involved in the treatment of these diseases.
基金supported by the National Natural Science Foundation of China,No.81671215(to XFY),No.31571002(to BGJ)the Natural Science Foundation of Beijing of China,No.7192215(to XFY)
文摘Peripheral nerve injury may trigger changes in mRNA levels in the spinal cord.Finding key mRNAs is important for improving repair after nerve injury.This study aimed to investigate changes in mRNAs in the spinal cord following sciatic nerve injury by transcriptomic analysis.The left sciatic nerve denervation model was established in C57 BL/6 mice.The left L4–6 spinal cord segment was obtained at 0,1,2,4 and 8 weeks after severing the sciatic nerve.mRNA expression profiles were generated by RNA sequencing.The sequencing results of spinal cord mRNA at 1,2,4,and 8 weeks after severing the sciatic nerve were compared with those at 0 weeks by bioinformatic analysis.We identified 1915 differentially expressed mRNAs in the spinal cord,of which 4,1909,and 2 were differentially expressed at 1,4,and 8 weeks after sciatic nerve injury,respectively.Sequencing results indicated that the number of differentially expressed mRNAs in the spinal cord was highest at 4 weeks after sciatic nerve injury.These mRNAs were associated with the cellular response to lipid,ATP metabolism,energy coupled proton transmembrane transport,nuclear transcription factor complex,vacuolar proton-transporting V-type ATPase complex,inner mitochondrial membrane protein complex,tau protein binding,NADH dehydrogenase activity and hydrogen ion transmembrane transporter activity.Of these mRNAs,Sgk1,Neurturin and Gpnmb took part in cell growth and development.Pathway analysis showed that these mRNAs were mainly involved in aldosterone-regulated sodium reabsorption,oxidative phosphorylation and collecting duct acid secretion.Functional assessment indicated that these mRNAs were associated with inflammation and cell morphology development.Our findings show that the number and type of spinal cord mRNAs involved in changes at different time points after peripheral nerve injury were different.The number of differentially expressed mRNAs in the spinal cord was highest at 4 weeks after sciatic nerve injury.These results provide reference data for finding new targets for the treatment of peripheral nerve injury,and for further gene therapy studies of peripheral nerve injury and repair.The study procedures were approved by the Ethics Committee of the Peking University People's Hospital(approval No.2017 PHC004)on March 5,2017.
基金Beijing Municipal science&Technology Commission(Grant No.2161100001816008)the National Natural Science Foundation of China(Grant No.31571403)Beijing Natural Science Foundation(Grant No.2171001)。
文摘Wang Shi Bao Chi Wan(WSBCW)is a traditional Chinese medicine with a recorded administration history of more than 180 years.In the present study,the preclinical safety of WSBCW was evaluated the preclinical safety of WSBCW using a toxicity test,which consisted of an administration period of 28 d and a recovery period of 15 d.During the test,male and female SD rats were administered the medicine once a day by oral gavage,at a dose of 60 mg/kg/day,600 mg/kg/day,or 1500 mg/kg/day.As a reference medicine,mosapride citrate was administered at a dose of 37.5 mg/kg/day,which was clinically equivalent to the high-dosage treatment of WSBCW.With all the dosage groups,statistically,no adverse effect was observed in terms of clinical observation,food intake,body weights,organ coefficient,blood biochemistry,and histopathology examination.No intestinal melanosis was observed in the rats.When the data were examined animal by animal,test substance-related adverse effects were found with the high-dosage rats in hematology assay.The deranged,however,reversible changes suggested a compromised intestinal barrier,which was also observed with in mosapride citrate-treated rats.In addition to the histopathology assay,molecular toxicology was explored using high-throughput gene sequencing.No evident toxicity was revealed.In summary,administration of WSBCW was well tolerated within a treatment of 28 d.
基金provided by the National Key Basic Research of China(2012CB114004)the Special Fund for Agro-Scientific Research in the Public Interest,China(201303021)the National R&D Project of Transgenic Crops of China(2012ZX08009001)
文摘Rice stripe virus（RSV） often causes severe rice yield loss in temperate regions of East Asia. Although the correlation of small interfering RNAs（si RNAs） with transgenic virus resistance of plants using RNA interference（RNAi） is known for decades, no systematical research has been done on the profiling of si RNAs from a genomic scale. Our research is aiming to systematically study the RNAi impact in RSV-resistant transgenic rice, which was generated by introducing an inverted repeat construct that targets RSV nucleocapsid protein（NCP） gene. In this paper, three independent RSV-retsistant transgenic rice lines were generated, their stable integration of the T-DNA fragment and the expression of si RNAs were confirmed by Southern blotting and Northern blotting analyses, and the majority of si RNAs were in lengths of 21, 22, and 24 nucleotides（nt）, which have validated a connection between the presence of the RSV NCP homologous si RNAs and the RSV resistance in those transgenic rice lines. In one of these transgenic lines（T4-B1）, the T-DNA fragment was found to have been inserted at chromosome 1 of the rice genome, substituting the rice genome fragment from 32 158 773 to 32 158 787 nt. Bioinformatics analysis of small RNA-Seq data on the T4-B1 line also confirmed the large population of NCP-derived si RNAs in transgenic plants, and the RSV-infected library（T4-B1-V） possessed more si RNAs than its mock inoculated libraries（T4-B1-VF）, these results indicating the inverted repeat construct and RSV could introduce abundance of si RNAs in transgenic rice. Moreover, a varied expression level of specific si RNAs was found among different segments of the NCP gene template, about 47% of NCP-derived si RNAs reads aligned with the fragment from 594 to 832 nt（239 nt in length） in NCP gene（969 nt in length） in the T4-B1-V, indicating a potential usage of hotspot regions for RNAi silencing in future research. In conclusion, as the first study to address the si RNA profile in RSV-resistant transgenic plant using next generation sequencing（NGS） technique, we confirmed that the massive abundance of si RNA derived from the inverted repeat of NCP is the major reason for RSV-resistance.
基金the National Natural Science Foundation of China(30871578)
文摘Two microRNA （miRNA） quantification methods, namely, poly（A） reverse transcription （RT）-quantitative real-time polymerase chain reaction （qPCR） and stem-loop RT-qPCR, have been developed for quantifying miRNA expression. In the present study, five miRNAs, including miR166, miR167, miR168, miR159, and miR396, with different sequence frequencies, were selected as targets to compare their expression profiles in five wheat tissues by applying the two methods and deep sequencing. The study aimed to determine a simple, reliable and high-throughput method for detecting miRNA expressions in wheat tissues. Results showed that the miRNA expression profiles determined by poly（A） RT-qPCR were more consistent with those obtained by deep sequencing. Further analysis indicated that the correlation coefficients of the data obtained by poly（A） RT-qPCR and deep sequencing （0.739, P≤0.01） were higher than those obtained by stem-loop RT-qPCR and deep sequencing （0.535, P≤0.01）. The protocol used for poly（A） RT-qPCR is simpler than that for stem-loop RT-qPCR. Thus, poly（A） RT-qPCR was a more suitable high-throughput assay for detecting miRNA expression profiles. To the best of our knowledge, this study was the first to compare these two miRNA quantification methods. We also provided useful information for quantifying miRNA in wheat or other plant species.
基金the National Natural Science Foundation of China(Nos.1137420,91129000,21273148,91229108,31370750 and 21303104)the National Basic Research Program(973) of China(No.2010CB529205)
文摘With the accomplishment of the genome draft sequences, identification of functional elements in genome has become an urgent task. Full-length cDNAs provide an important resource for gene identification and their precise structural feature determination. It also provides a basis for genomic element definition. As many regulatory elements are around transcription start sites(TSSs), precise localization of TSSs in the genome becomes a critical step for identifying the associated core promoters. Massive parallel snapshot of TSSs at a particular time under a specific experimental condition makes it possible to globally analyze important regulatory elements around TSSs and further construct transcriptional regulatory networks. In this paper, we first reviewed two important full-length cDNA cloning techniques: cap-trapper technique and oligo-capping technique. Then,we introduced deepCAGE, a cap-trapper and deep sequencing-based TSS profiling technique, and its applications in the research of transcriptional regulation.
文摘This is the first systematic investigation of viral pathogens in <i>Vitis</i> <i>vinifera</i> from Hangzhou vicinity of China. About 7 viruses and 5 viroids were annotated from four production bases “Dushicun”, “Wangjiayuan”, “Xiajiangcun”, and “Yangducun” covering 15 cultivars through sRNAseq technique. At least 3 viruses<a name="OLE_LINK4"></a>—grapevine leaf roll-associated virus 3 (GLRaV-3), grapevine fleck <span>virus (GFkV) and grapevine geminivirus A (GGVA), and 4 viroids—hop stunt</span> viroid (HSVd), citrus viroid II (CVd-II), grapevine yellow speckle viroid 1 (GYSVd-1) and grapevine yellow speckle viroid 2 (GYSVd-2) infected all four bases. “Yangducun” base showed 11, the most infected pathogens. GYSVd-1 showed the highest accumulation in host of Wangjiayuan base. The main in<span>fected pathogens were verified by reverse-transcription polymerase chain reaction</span> (RT-PCR) technique, the detected rate reached to 85% - 100%. The results provide an important basis for effective and precise detection of viral diseases in the area and for the virus-free cultivation in future.
基金supported by the National Natural Science Foundation of China(81790643,81970839,82271105,82121003)the Sichuan Science and Technology Program(2021YFS0033,2021YFS0369,2021YFS0404,2021JDGD0036)the Chinese Academy of Medical Sciences(CAMS)Innovation Fund for Medical Sciences(2019I2M-5-032)。
文摘The human retina serves as a light detector and signals transmission tissue.Advanced insights into retinal disease mechanisms and therapeutic strategies require a deep understanding of healthy retina molecular events.Here,we sequenced the m RNA of over 0.6 million single cells from human retinas across six regions at nine different ages.Sixty cell sub-types have been identified from the human mature retinas with unique markers.We revealed regional and age differences of gene expression profiles within the human retina.Cell-cell interaction analysis indicated a rich synaptic connection within the retinal cells.Gene expression regulon analysis revealed the specific expression of transcription factors and their regulated genes in human retina cell types.Some of the gene’s expression,such as DKK3,are elevated in aged retinas.A further functional investigation suggested that over expression of DKK3 could impact mitochondrial stability.Overall,decoding the molecular dynamic architecture of the human retina improves our understanding of the vision system.
基金supported by CAMS Innovation Fund for Medical Sciences(2016-I2M-1-014,2017-I2M-3-017)the National Major Science&Technology Project for Control and Prevention of Major Infectious Diseases in China(2017ZX10103004,2018ZX10305409,2018ZX10301401,2018ZX10732401)Fondation Mérieux.The funders had no role in study design,data collection and analysis,decision to publish,or preparation of the manuscript.
文摘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.
基金supported by grants from the China National Basic Research Program(2010CB126002)the National Natural Science Foundation of China(90717009)the 111 Project funded by the Chinese Ministry of Education
文摘We assembled a total of 297,239 Gossypium hirsutum （Gh, a tetraploid cotton, AADD） expressed sequence tag （EST） sequences that were available in the National Center for Biotechnology Information database, with reference to the recently published G. raimondii （Gr, a diploid cotton, DD） genome, and obtained 49,125 UniGenes. The average lengths of the U niGenes were increased from 804 and 791 bp in two previous EST assemblies to 1,019 bp in the current analysis. The number of putative cotton UniGenes with lengths of 3 kb or more increased from 25 or 34 to 1,223. As a result, thousands of originally independent G. hirsutum ESTs were aligned to produce large contigs encoding transcripts with very long open reading frames, indicating that the G. raimondii genome sequence provided remarkable advantages to assemble the tetraploid cotton transcriptome. Significant different distribution patterns within several GO terms, including transcription factor activity, were observed between D- and A-derived assemblies. Tran- scriptome analysis showed that, in a tetraploid cotton cell, 29,547 UniGenes were possibly derived from the D subgenome while another 19,578 may come from the A subgenome. Finally, some of the in silico data were confirmed by reverse transcription polymerase chain reaction experiments to show the changes in transcript levels for several gene families known to play key role in cotton fiber development. We believe that our work provides a useful platform for functional and evolutionary genomic studies in cotton.
