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Adaptive nanopores:A bioinspired label-free approach for protein sequencing and identification 认领
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作者 Andrea Spitaleri Denis Garoli +3 位作者 Moritz Schutte Hans Lehrach Walter Rocchia Francesco De Angelis 《纳米研究:英文版》 SCIE EI CAS 2021年第1期328-333,共6页
Single molecule protein sequencing would tremendously impact in proteomics and human biology and it would promote the development of novel diagnostic and therapeutic approaches.However,its technological realization ca... Single molecule protein sequencing would tremendously impact in proteomics and human biology and it would promote the development of novel diagnostic and therapeutic approaches.However,its technological realization can only be envisioned,and huge challenges need to be overcome.Major difficulties are inherent to the structure of proteins,which are composed by several different amino-acids.Despite long standing efforts,only few complex techniques,such as Edman degradation,liquid chromatography and mass spectroscopy,make protein sequencing possible.Unfortunately,these techniques present significant limitations in terms of amount of sample required and dynamic range of measurement.It is known that proteins can distinguish closely similar molecules.Moreover,several proteins can work as biological nanopores in order to perform single molecule detection and sequencing.Unfortunately,while DNA sequencing by means of nanopores is demonstrated,very few examples of nanopores able to perform reliable protein-sequencing have been reported sofar.Here,we investigate,by means of molecular dynamics simulations,how a re-engineered protein,acting as biological nanopore,can be used to recognize the sequence of a translocating peptide by sensing the MshapeH of individual amino-acids.In our simulations we demonstrate that it is possible to discriminate with high fidelity,9 different amino-acids in a short peptide translocating through the engineered construct.The method,here shown for fluorescence-based sequencing,does not require any labelling of the peptidic analyte.These results can pave the way for a new and highly sensitive method of sequencing. 展开更多
关键词 NANOPORES single molecule sequencing protein sequencing luorescence resonance energy transfer(FRET) amino-acids fluorescence
An Experimental Study on Bio-Clogging in Porous Media during Geothermal Water Reinjection 认领
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作者 Jianguo Feng Yao Zhao +1 位作者 Deshuai Ji Zongjun Gao 《水资源与保护(英文)》 2021年第2期139-153,共15页
To study the mechanism of bio-clogging in a porous medium during the reinjection of geothermal water and to improve reinjection efficiency, an indoor one-dimensional reinjection experiment was conducted based on the g... To study the mechanism of bio-clogging in a porous medium during the reinjection of geothermal water and to improve reinjection efficiency, an indoor one-dimensional reinjection experiment was conducted based on the geological model of the geothermal reinjection demonstration project in Dezhou City. The biological process of porous media clogging was investigated by analyzing the variation of permeability within the medium, the main indexes of nutrient salts, and the content of extracellular polymeric substances (EPS). High-throughput sequencing, based on 16S rRNA, was used to analyze the characteristics and succession of microbial communities during the reinjection of geothermal water. The results of the study show that significant bio-clogging occurs during the reinjection of geothermal water, with an increase in the heterogeneity of the thermal reservoir medium, and a decrease in permeability. The extent of clogging gradually reduces with an increase in seepage path. Thus, thermal reservoir clogging is more serious closer to the water inlet. With an increase in the duration of reinjection, the permeability of the porous medium undergoes three stages: “rapid”, “decline-slow”, and “decrease-stable”. The results show that the richness and diversity of the bacterial community increase and decrease, respectively, during the reinjection process. Bacterial community succession occurs, and the bacterial communities mainly include the Proteobacteria and Bacteroidetes phyla. <em>Pseudomonas</em> and <em>Devosia</em> are respectively the dominant bacteria in the early and late stages of geothermal water reinjection. 展开更多
关键词 Geothermal Water Reinjection Bio-Clogging Indoor Experiment High-Throughput Sequencing
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Isolation and Characterization of Native Rhizobium Strains Nodulating Some Legumes Species in South Brazzaville in Republic of Congo 认领
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作者 Mabiala Shaloom Teresa Joseph Goma-Tchimbakala +1 位作者 Nzaou Stech Anomene Eckzechel Lebonguy Augustin Aimé 《生命科学与技术进展(英文)》 2021年第1期10-30,共21页
Actually, in Republic of Congo, rhizobia have poorly phenotypically and biochemically characterized. This study aimed to characterize native rhizobia. Rhizobia strains were isolated using nodule roots collected on <... Actually, in Republic of Congo, rhizobia have poorly phenotypically and biochemically characterized. This study aimed to characterize native rhizobia. Rhizobia strains were isolated using nodule roots collected on <i><span style="font-family:Verdana;">Milletia laurentii</span></i><span style="font-family:Verdana;">, </span><i><span style="font-family:Verdana;">Acacia spp</span></i><span style="font-family:Verdana;">., </span><i><span style="font-family:Verdana;">Albizia lebbeck</span></i><span style="font-family:Verdana;">,</span><i> </i><span style="font-family:Verdana;">and</span><i><span style="font-family:Verdana;"> Vigna unguiculata</span></i><span style="font-family:Verdana;">. The strains isolated were characterized microbiologically, biochemically, physiologically, and molecularly identified using 16S rRNA method. The results reported in this study are only for six strains of all 77 isolated: RhA1, RhAc4, RhAc15, RhAc13, RhW1, and RhV3. All native strains were positive to urease activity, negative to cellulase and pectinase activity except for one isolate that showed a positive cellulase activity. Moreover, isolates have grown at 12% of NaCl. On different effects of temperatures, isolates were able to grow up to 44</span><span style="font-family:;" "=""><span style="font-family:Verdana;">°C and showed good growth at pH from 7 to 9 and the ability to use ten different carbon hydrates sources. The strains were identified as </span><i><span style="font-family:Verdana;">Rhizobium tropici</span></i><span style="font-family:Verdana;">, </span><i><span style="font-family:Verdana;">Rhizobium sp</span></i><span style="font-family:Verdana;">., </span><i><span style="font-family:Verdana;">Mesorhizobium sp</span></i><span style="font-family:Verdana;">. </span><i><span style="font-family:Verdana;">Bradyrhizobium yuanmingense</span></i><span style="font-family:Verdana;"> and </span><i><span style="font-family:Verdana;">Bradyrhizobium elkanii</span></i><span style="font-family:Verdana;">. The phylogenetically analysis 展开更多
关键词 RHIZOBIA Milletia laurentii Acacia spp. Albizia lebbeck Vigna unguiculata 16S rRNA Sequencing
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Current scenario of the genetic testing for rare neurological disorders exploiting next generation sequencing 认领
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作者 Chiara Di Resta Giovanni Battista Pipitone +1 位作者 Paola Carrera Maurizio Ferrari 《中国神经再生研究:英文版》 SCIE CAS 2021年第3期475-481,共7页
Next generation sequencing is currently a cornerstone of genetic testing in routine diagnostics,allowing for the detection of sequence variants with so far unprecedented large scale,mainly in genetically heterogenous ... Next generation sequencing is currently a cornerstone of genetic testing in routine diagnostics,allowing for the detection of sequence variants with so far unprecedented large scale,mainly in genetically heterogenous diseases,such as neurological disorders.It is a fast-moving field,where new wet enrichment protocols and bioinformatics tools are constantly being developed to overcome initial limitations.Despite the as yet undiscussed advantages,however,there are still some challenges in data analysis and the interpretation of variants.In this review,we address the current state of next generation sequencing diagnostic testing for inherited human disorders,particularly giving an overview of the available high-throughput sequencing approaches;including targeted,whole-exome and whole-genome sequencing;and discussing the main critical aspects of the bioinformatic process,from raw data analysis to molecular diagnosis. 展开更多
关键词 clinical practice genetic testing NEUROGENESIS next generation sequencing sequencing approaches variant interpretation
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Complementary DNA sequencing (cDNA): an eff ective approach for assessing the diversity and distribution of marine benthic ciliates along hydrographic gradients 认领
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作者 Pingping HUANG Feng ZHAO Kuidong XU 《海洋湖沼学报(英文)》 SCIE CAS 2021年第1期208-222,共15页
The Yellow Sea Cold Water Mass(YSCWM)is a distinct hydrographic phenomenon of the Yellow Sea,and the distribution pattern of meio-and macrobenthos diff ers inside and outside of the YSCWM.However,such a pattern has ne... The Yellow Sea Cold Water Mass(YSCWM)is a distinct hydrographic phenomenon of the Yellow Sea,and the distribution pattern of meio-and macrobenthos diff ers inside and outside of the YSCWM.However,such a pattern has never been observed in the microbenthic ciliate communities.Therefore,we hypothesized that benthic ciliates followed a similar distribution pattern as meio-and macrobenthos,but this pattern has not been uncovered by morphological methods.We evaluated the diversity and distribution of benthic ciliates at fi ve stations along hydrographic gradients across the YSCWM and adjacent shallow water by using morphology and DNA and complementary DNA(cDNA)high-throughput sequencing of the V4 region of 18S rRNA gene.Results showed that the diversity of benthic ciliates detected by DNA(303 OTUs),and the cDNA(611 OTUs)sequencing was much higher than that detected by the morphological method(79 species).Morphological method detected roughly diff erent ciliate communities inside and outside of the YSCWM,but without statistical signifi cance.No clear pattern was obtained by DNA sequencing.In contrast,cDNA sequencing revealed a distinct distribution pattern of benthic ciliate communities like meioand macrobenthos,which coincided well with the results of the environmental parameter analysis.More than half of the total sequences detected by DNA sequencing belonged to planktonic ciliates,most(if not all)of which were recovered from historic DNA originating through the sedimentation of pelagic forms because none of them were observed morphologically.The irrelevant historic DNA greatly infl uenced the recovery of rare species and thus limited the understanding of the benthic ciliate diversity and distribution.Our research indicates that the methods used have signifi cant eff ects on the investigation of benthic ciliate communities and highlights that cDNA sequencing has great advantages in estimating the diversity and distribution of benthic ciliates,as well as the potential for benthic environmental assessments. 展开更多
关键词 benthic ciliates cDNA high-throughput sequencing community comparison DNA highthroughput sequencing morphology
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Application of 16s rDNA Sequencing in the Analysis of Pathogenic Bacteria in Sputum of Severe Bacterial Pneumonia 认领
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作者 Jun Zheng Juan Zhu +4 位作者 Bin Chen Lingxiu Chen Tian Gao Xinping Chen Tao Huang 《微生物学(英文)》 2021年第2期109-116,共8页
<b>Objective:</b> 120 patients with severe pneumonia who were kept in the comprehensive ICU of our hospital in 2018 were selected, and 16s rDNA sequencing was performed to analyze the composition of pathog... <b>Objective:</b> 120 patients with severe pneumonia who were kept in the comprehensive ICU of our hospital in 2018 were selected, and 16s rDNA sequencing was performed to analyze the composition of pathogenic bacteria in the sputum of severe pneumonia. <b>Methods:</b> The sputum samples of patients with severe bacterial pneumonia were collected, and the diversity of pathogens in the samples was analyzed by polymerase chain reaction (PCR) amplification and high-throughput sequencing (16s rDNA PCR-DGGE). <b>Results:</b> Sequence showed that sputum samples contained a relatively large number of species, and there were many species that were not detected by sequencing. The dominant bacteria were <i>Streptococcus, Sphingomonas, Corynebacterium, Denatobacteria, Aquobacteria, Acinetobacteria, Prevotella, Klebsiella, Pseudomonas</i>, etc. <b>Conclusion:</b> Bacteria caused by sputum of severe bacterial pneumonia are complex and diverse, which provides new methods and ideas for individualized treatment of patients with severe pneumonia. 展开更多
关键词 Bacterial Severe Pneumonia SPUTUM The Pathogenic Bacterium 16s rDNA Sequencing
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文章速递香蕉秸秆不同还田模式对土壤微生物群落的影响 认领
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作者 孙鹏 刘满意 王蓓蓓 《热带生物学报》 2021年第1期57-62,共6页
采用土壤室内培养的方法,以香蕉秸秆不同还田模式为试验唯一变量因素,设置3个处理(无秸秆还田CK;将香蕉秸秆覆盖到土壤表层,作为秸秆自然还田处理F;将土壤与香蕉秸秆彻底混合,作为秸秆掩埋还田处理T),分析香蕉秸秆不同还田模式下的微生... 采用土壤室内培养的方法,以香蕉秸秆不同还田模式为试验唯一变量因素,设置3个处理(无秸秆还田CK;将香蕉秸秆覆盖到土壤表层,作为秸秆自然还田处理F;将土壤与香蕉秸秆彻底混合,作为秸秆掩埋还田处理T),分析香蕉秸秆不同还田模式下的微生物群落差异,以期揭示香蕉秸秆的不同还田模式对土壤微生物的影响。结果表明:T、F处理与CK处理相比,真菌门中Basidiomycota相对丰度分别增加1.3%和2.8%;细菌门中Acidobacteria相对丰度分别增加5.1%和1.1%,Actinobacteria的相对丰度分别增加1.9%和3.2%。处理间Fusarium相对丰度大小顺序为CK>F>T。处理间细菌群落的丰富度(SChao1)和多样性(HShannon)大小顺序均为T>F>CK,真菌群落并无明显差异。聚类分析表明,T处理土壤微生物群落结构与CK处理明显不同。主坐标分析和OTU数量分布结果表明,T处理土壤微生物群落结构与F处理相近。本研究结果显示,T处理增加了土壤细菌群落的丰富性与多样性,改变了土壤微生物的群落结构,同时提高了具有分解功能的微生物分类属的相对丰度,并显著降低了病原菌的相对丰度。 展开更多
关键词 香蕉秸秆 微生物群落结构 微生物群落多样性 微生物群落丰富度 MiSeq sequencing 秸秆还田模式
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文章速递Application of 16S rDNA Sequencing Technology in the Analysis of Pathogenic Bacteria in Sputum of Severe Pneumonia 认领
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作者 Jun Zheng Juan Zhu +4 位作者 Bin Chen Lingxiu Chen Tian Gao Xinping Chen Feiyan Li 《微生物学(英文)》 2021年第3期157-164,共8页
The diagnosis of pathogenic bacteria in severe pneumonia is difficult and the prognosis is poor. Its outcome is closely related to bacterial pathogenicity and the timeliness and pertinence of antibiotic treatment. The... The diagnosis of pathogenic bacteria in severe pneumonia is difficult and the prognosis is poor. Its outcome is closely related to bacterial pathogenicity and the timeliness and pertinence of antibiotic treatment. Therefore, early diagnosis is of great significance to the prognosis of patients. Sputum examination and culture is the gold standard for the diagnosis of pathogens of severe pneumonia. However, due to the long time of bacterial culture, the early use of antibiotics, the change of bacteria species, mixed infection and other problems, the results of bacterial culture in sputum are often false negative. With the continuous application of new molecular biology techniques in clinical detection, the classification of bacteria and microorganisms has deepened from the identification of phenotypic characteristics to the classification of gene characteristics. Sequencing analysis with 16S rDNA sequencing technology has the characteristics of high sequencing flux, large amount of data obtained, short cycle, and can more comprehensively reflect the species composition of microbial community, real species distribution and abundance information. In this paper, 16S rDNA sequencing technology was used to analyze the bacterial population composition in the sputum of severe pneumonia, and to explore a new method of etiological diagnosis. 展开更多
关键词 Bacterial Severe Pneumonia Sputum The Pathogenic Bacterium 16S rDNA Sequencing
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MicroRNA and mRNA profiling of cerebral cortex in a transgenic mouse model of Alzheimer’s disease by RNA sequencing 认领
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作者 Li Zeng Hai-Lun Jiang +2 位作者 Ghulam Md Ashraf Zhuo-Rong Li Rui Liu 《中国神经再生研究:英文版》 SCIE CAS 2021年第10期2099-2108,共10页
In a previous study,we found that long non-coding genes in Alzheimer’s disease(AD)are a result of endogenous gene disorders caused by the recruitment of microRNA(miRNA)and mRNA,and that miR-200a-3p and other represen... In a previous study,we found that long non-coding genes in Alzheimer’s disease(AD)are a result of endogenous gene disorders caused by the recruitment of microRNA(miRNA)and mRNA,and that miR-200a-3p and other representative miRNAs can mediate cognitive impairment and thus serve as new biomarkers for AD.In this study,we investigated the abnormal expression of miRNA and mRNA and the pathogenesis of AD at the epigenetic level.To this aim,we performed RNA sequencing and an integrative analysis of the cerebral cortex of the widely used amyloid precursor protein and presenilin-1 double transgenic mouse model of AD.Overall,129 mRNAs and 68 miRNAs were aberrantly expressed.Among these,eight down-regulated miRNAs and seven up-regulated miRNAs appeared as promising noninvasive biomarkers and therapeutic targets.The main enriched signaling pathways involved mitogen-activated kinase protein,phosphatidylinositol 3-kinase-protein kinase B,mechanistic target of rapamycin kinase,forkhead box O,and autophagy.An miRNA-mRNA network between dysregulated miRNAs and corresponding target genes connected with AD progression was also constructed.These miRNAs and mRNAs are potential biomarkers and therapeutic targets for new treatment strategies,early diagnosis,and prevention of AD.The present results provide a novel perspective on the role of miRNAs and mRNAs in AD.This study was approved by the Experimental Animal Care and Use Committee of Institute of Medicinal Biotechnology of Beijing,China(approval No.IMB-201909-D6)on September 6,2019. 展开更多
关键词 3ʹ-untranslated region Alzheimer’s disease BIOMARKER cerebral cortex Gene Ontology high-throughput sequencing intracellular neurofibrillary tangles microtubule-associated protein-τ miRNA-mRNA network presenilin 1
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测序技术在结直肠癌研究中的应用 认领
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作者 杨长江 申占龙 +1 位作者 叶颖江 王杉 《中华实验外科杂志》 CAS 北大核心 2021年第2期392-396,共5页
测序技术的出现是分子生物学领域的伟大变革,该技术已经被广泛应用于各类疾病的研究并取得了重大突破。结直肠癌是一种涉及到多种基因表达改变的疾病,高通量测序技术在结直肠癌基因组、转录组、循环肿瘤DNA及表观遗传学研究中发挥了重... 测序技术的出现是分子生物学领域的伟大变革,该技术已经被广泛应用于各类疾病的研究并取得了重大突破。结直肠癌是一种涉及到多种基因表达改变的疾病,高通量测序技术在结直肠癌基因组、转录组、循环肿瘤DNA及表观遗传学研究中发挥了重大作用,为人类从更深层次认识结直肠癌的发生发展机制,更好的指导临床诊疗做出了巨大贡献。本文就测序技术在结直肠癌研究中的应用做简要综述。 展开更多
关键词 结直肠癌 测序 遗传变异
A chromosome-level genome assembly of the wild rice Oryza rufipogon facilitates tracing the origins of Asian cultivated rice 认领
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作者 Xianrong Xie Huilong Du +7 位作者 Huiwu Tang Jianian Tang Xiyu Tan Weizhi Liu Tie Li Zhansheng Lin Chengzhi Liang Yao-Guang Liu 《中国科学:生命科学英文版》 SCIE CAS 2021年第2期282-293,共12页
Oryza rufipogon Griff.is a wild progenitor of the Asian cultivated rice Oryza sativa.To better understand the genomic diversity of the wild rice,high-quality reference genomes of O.rufipogon populations are needed,whi... Oryza rufipogon Griff.is a wild progenitor of the Asian cultivated rice Oryza sativa.To better understand the genomic diversity of the wild rice,high-quality reference genomes of O.rufipogon populations are needed,which also facilitate utilization of the wild genetic resources in rice breeding.In this study,we generated a chromosome-level genome assembly of O.rufipogon using a combination of short-read sequencing,single-molecule sequencing,BioNano and Hi-C platforms.The genome sequence(399.8 Mb)was assembled into 46 scaffolds on the 12 chromosomes,with contig N50 and scaffold N50 of 13.2 Mb and 20.3 Mb,respectively.The genome contains 36,520 protein-coding genes,and 49.37% of the genome consists of repetitive elements.The genome has strong synteny with those of the O.sativa subspecies indica and japonica,but containing some large structural variations.Evolutionary analysis unveiled the polyphyletic origins of O.sativa,in which the japonica and indica genome formations involved different divergent O.rufipogon(including O.nivara)lineages,accompanied by introgression of genomic regions between japonica and indica.This high-quality reference genome provides insight on the genome evolution of the wild rice and the origins of the O.sativa subspecies,and valuable information for basic research and rice breeding. 展开更多
关键词 GENOME genome sequencing EVOLUTION Oryza rufipogon RICE
利用SLAF-seq结合BSA方法发掘大豆种皮色相关基因 认领
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作者 郁晓敏 金杭霞 +4 位作者 杨清华 傅旭军 郭丹丹 吕晓男 袁凤杰 《分子植物育种》 CAS 北大核心 2021年第2期385-391,共7页
种皮色不仅是一个形态标记,还是一种重要的进化性状,与大豆商品性、营养价值以及抗性关系密切。本研究以黄色种皮大豆品系BMY及其褐色种皮衍生品系BMZ为亲本,从F2群体中分别挑选出黄色种皮和褐色种皮的植株各9株,构建了两个极端性状混合... 种皮色不仅是一个形态标记,还是一种重要的进化性状,与大豆商品性、营养价值以及抗性关系密切。本研究以黄色种皮大豆品系BMY及其褐色种皮衍生品系BMZ为亲本,从F2群体中分别挑选出黄色种皮和褐色种皮的植株各9株,构建了两个极端性状混合池DNA文库,借助SLAF-seq和BSA技术,挖掘大豆种皮色性状相关候选基因。对于26121个高质量SNP位点,利用SNP-index方法和ED方法进行综合分析,获得8个与目标性状紧密关联的候选区域,分别位于第5、11、12、19和20染色体,包含620个编码基因。对这620个基因进行进一步的功能注释,NR、Swiss-Prot、GO、KEGG和COG数据库分别注释到600、518、533、133和256个基因,其中存在非同义突变基因4个,分别为Glyma05g005600、Glyma05g009700、Glyma12g006100和Glyma12g047300。候选区域内编码基因的深度注释有助于功能基因的进一步分离,为大豆种皮色性状相关基因的精细定位及克隆提供理论依据。 展开更多
关键词 大豆 种皮色 重测序 关联分析
Severe community-acquired pneumonia caused by Leptospira interrogans:A case report and review of literature 认领
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作者 Qiu-Hong Bao Li Yu +4 位作者 Jian-Jun Ding Ying-Jun Chen Jun-Wei Wang Jian-Ming Pang Qi Jin 《世界临床病例杂志》 SCIE 2021年第8期1901-1908,共8页
BACKGROUND Leptospira is an uncommon pathogen for adult severe community-acquired pneumonia and its nonspecific manifestations and limited diagnostic tests make it difficult to identify.Although conventional penicilli... BACKGROUND Leptospira is an uncommon pathogen for adult severe community-acquired pneumonia and its nonspecific manifestations and limited diagnostic tests make it difficult to identify.Although conventional penicillin remains efficacious to treat leptospirosis,failure in early diagnosis and treatment can lead to progression into a deadly syndrome with multiple organ dysfunction.Next generation sequencing is of great value to understand cases with infection of unknown cause,which could help in the diagnosis of uncertain Leptospira infection.CASE SUMMARY We recently managed a patient with fever,cough and dyspnea on admission that progressed into persistent adult respiratory distress syndrome,hemoptysis and hematuria after admission.In this case,the rare Leptospira infection was clouded by the positive influenza tests at admission,delaying early Leptospira-targeted antibiotics administration.Next generation sequencing,a novel molecular diagnostic tool,provided a key hint to uncover the crucial pathogen,Leptospira interrogans,further supported by the possible occupational exposure history.Subsequent conventional penicillin and mechanical respiratory support were administrated to cure the patient successfully without any sequela.CONCLUSION Clinicians must pay attention to possible exposure history and keep uncommon Leptospira in mind when managing pneumonia with unknown causes. 展开更多
关键词 Leptospira interrogans PNEUMONIA Next generation sequencing INFLUENZA DIAGNOSIS Case report
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Eff ects of viral infection and microbial diversity on patients with sepsis:A retrospective study based on metagenomic next-generation sequencing 认领
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作者 Li-wei Duan Jin-long Qu +13 位作者 Jian Wan Yong-hua Xu Yi Shan Li-xue Wu Jin-hao Zheng Wei-wei Jiang Qi-tong Chen Yan Zhu Jian Zhou Wen-bo Yu Lei Pei Xi Song Wen-fang Li Zhao-fen Lin 《世界急诊医学杂志(英文)》 SCIE CAS 2021年第1期29-35,共7页
BACKGROUND: The study aims to investigate the performance of a metagenomic next-generationsequencing (NGS)-based diagnostic technique for the identifi cation of potential bacterial and viral infectionsand eff ects of ... BACKGROUND: The study aims to investigate the performance of a metagenomic next-generationsequencing (NGS)-based diagnostic technique for the identifi cation of potential bacterial and viral infectionsand eff ects of concomitant viral infection on the survival rate of intensive care unit (ICU) sepsis patients.METHODS: A total of 74 ICU patients with sepsis who were admitted to our institution from February1, 2018 to June 30, 2019 were enrolled. Separate blood samples were collected from patients for bloodcultures and metagenomic NGS when the patients’ body temperature was higher than 38 °C. Patients’demographic data, including gender, age, ICU duration, ICU scores, and laboratory results, were recorded.The correlations between pathogen types and sepsis severity and survival rate were evaluated.RESULTS: NGS produced higher positive results (105 of 118;88.98%) than blood cultures(18 of 118;15.25%) over the whole study period. Concomitant viral infection correlated closelywith sepsis severity and had the negative effect on the survival of patients with sepsis. However,correlation analysis indicated that the bacterial variety did not correlate with the severity of sepsis.CONCLUSIONS: Concurrent viral load correlates closely with the severity of sepsis and thesurvival rate of the ICU sepsis patients. This suggests that prophylactic administration of antiviraldrugs combined with antibiotics may be benefi cial to ICU sepsis patients. 展开更多
关键词 SEPSIS Metagenomic next-generation sequencing Viral infections Bacterial infections Microbial diversity
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Single-Cell Transcriptome Analysis in Plants:Advances and Challenges 认领
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作者 Rahul Shaw Xin Tian Jian Xu 《分子植物:英文版》 SCIE CAS 2021年第1期115-126,共12页
The rapid and enthusiastic adoption of single-cell RNA sequencing(scRNA-seq)has demonstrated that this technology is far more than just another way to perform transcriptome analysis.It is not an exaggeration to say th... The rapid and enthusiastic adoption of single-cell RNA sequencing(scRNA-seq)has demonstrated that this technology is far more than just another way to perform transcriptome analysis.It is not an exaggeration to say that the advent of scRNA-seq is revolutionizing the details of whole-transcriptome snapshots from a tissue to a cell.With this disruptive technology,it is now possible to mine heterogeneity between tissue types and within cells like never before.This enables more rapid identification of rare and novel cell types,simultaneous characterization of multiple different cell types and states,more accurate and integrated understanding of their roles in life processes,and more.However,we are only at the beginning of unlocking the full potential of scRNA-seq applications.This is particularly true for plant sciences,where single-cell transcriptome profiling is in its early stage and has many exciting challenges to overcome.In this review,we compare and evaluate recent pioneering studies using the A rabidopsis root model,which has established new paradigms for scRNA-seq studies in plants.We also explore several new and promising single-cell analysis tools that are available to those wishing to study plant development and physiology at unprecedented resolution and scale.In addition,we propose some future directions on the use of scRNA-seq technology to tackle some of the critical challenges in plant research and breeding. 展开更多
关键词 bioinformatics pipelines cell types and states plant development and physiology single-cell RNA sequencing single-cell transcriptome analysis
Human parvovirus B19-associated early postoperative acquired pure red cell aplasia in simultaneous pancreas-kidney transplantation:A case report 认领
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作者 Hui Wang Ying-Xin Fu +5 位作者 Wen-Li Song Zhen Wang Gang Feng Jie Zhao Ye-Qi Nian Yu Cao 《世界临床病例杂志》 SCIE 2021年第8期1968-1975,共8页
BACKGROUND Acquired pure red cell aplasia(aPRCA)related to human parvovirus B19(HPV B19)is rarely reported in simultaneous pancreas-kidney transplantation(SPKT)recipients;there has yet to be a case report of early pos... BACKGROUND Acquired pure red cell aplasia(aPRCA)related to human parvovirus B19(HPV B19)is rarely reported in simultaneous pancreas-kidney transplantation(SPKT)recipients;there has yet to be a case report of early postoperative infection.In this current study,we report the case of a Chinese patient who experienced the disease in the early postoperative period.CASE SUMMARY A 63-year-old man,with type 2 diabetes and end-stage renal disease,received a brain dead donor-derived SPKT.Immunosuppression treatment consisted of tacrolimus,prednisone,enteric-coated mycophenolate sodium(EC-MPS),and thymoglobulin combined with methylprednisolone as induction.The hemoglobin(Hb)level declined due to melena at postoperative day(POD)3,erythropoietinresistant anemia persisted,and reticulocytopenia was diagnosed at POD 20.The bone marrow aspirate showed decreased erythropoiesis and the presence of giant pronormoblasts at POD 43.Metagenomic next-generation sequencing(mNGS)of a blood sample identified HPV B19 infection at POD 66.EC-MPS was withdrawn;three cycles of intravenous immunoglobulin(IVIG)infusion therapy were administered;and tacrolimus was switched to cyclosporine.The HPV B19-associated aPRCA resolved completely and did not relapse within the 1-year follow-up period.The diminution in mNGS reads was correlated with Hb and reticulocyte count improvements.CONCLUSION HPV B19-associated aPRCA can occur at an early period after SPKT.An effective therapy regimen includes IVIG infusion and adjustment of the immunosuppressive regimen.Moreover,mNGS can be used for the diagnosis and to reflect disease progression. 展开更多
关键词 ANEMIA Human parvovirus B19 Intravenous immunoglobulin METAGENOMIC Next-generation sequencing Pancreas transplantation Case report
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Coinheritance of OLFM2 and SIX6 variants in a Chinese family with juvenile-onset primary open-angle glaucoma: A case report 认领
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作者 Xue Yang Nan-Nan Sun +6 位作者 Zhen-Ni Zhao Shu-Xiang He Miao Zhang Dan-Dan Zhang Xiao-Wei Yu Jia-Min Zhang Zhi-Gang Fan 《世界临床病例杂志》 SCIE 2021年第3期697-706,共10页
BACKGROUND Juvenile-onset primary open-angle glaucoma(JOAG),characterized by severe elevation of intraocular pressure and optic neuropathy prior to the age of 40,is a rare subtype of primary open-angle glaucoma.Severa... BACKGROUND Juvenile-onset primary open-angle glaucoma(JOAG),characterized by severe elevation of intraocular pressure and optic neuropathy prior to the age of 40,is a rare subtype of primary open-angle glaucoma.Several genetic mutations have been associated with JOAG.CASE SUMMARY The proband patient was a young male,diagnosed with primary open-angle glaucoma at the age of 27.The patient and his unaffected parents who have been excluded from classic genetic mutations for primary open-angle glaucoma were included to explore for other possible genetic variants through whole genome sequencing and bioinformatics analysis.In this trio,we found two heterozygous variants inherited from the parents in the proband:c.281G>A,p.Arg94His in OLFM2 and c.177C>G,p.Ile59Met in SIX6.Both genetic mutations are predicted through bioinformatics analysis to replace evolutionary conserved amino acids,therefore rendering a pathogenic effect on proteins.In contrast,very low frequencies for these genetic mutations were recorded in most common control databases.CONCLUSION This is the first report on coinherited mutations of OLFM2 and SIX6 in a JOAG family,which shows the complexity of JOAG inheritance.Large-scale clinical screening and molecular functional investigations on these coinherited mutations are imperative to improve our understanding of the development of JOAG. 展开更多
关键词 Juvenile-onset primary open-angle glaucoma Whole genome sequencing Coinheritance OLFM2 SIX6 Case report
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Epiphytic and Endophytic Fungal Communities of Tomato Plants 认领
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作者 Chunjuan Dong Lingling Wang +1 位作者 Qian Li Qingmao Shang 《Horticultural Plant Journal(园艺学报:英文版)》 SCIE 2021年第1期38-48,共11页
Plants harbor diverse fungal communities both on their surfaces(epiphytic)and inside of plant tissues(endophytic),and these fungi play important roles in plant health and vigor.However,comparisons of epiphytes and end... Plants harbor diverse fungal communities both on their surfaces(epiphytic)and inside of plant tissues(endophytic),and these fungi play important roles in plant health and vigor.However,comparisons of epiphytes and endophytes have rarely been performed.In this study,the soil,epiphytic and endophytic fungal assemblages of greenhouse-grown tomato plants were extensively examined and compared by Illumina sequencing of 18S rRNA amplicons.The fungal communities differed in both size and composition.The soil communities were the richest and most abundant,while the endophytes showed the lowest richness and diversity.The diversity of endophytes also differed in different tissues,with the highest diversity occurring in the roots.In both the epiphytic and endophytic samples,the majority of fungi corresponded to ascomycetes,amongwhich Sordariomycetes,Dothideomycetes and Eurotiomyceteswere the most frequent classes.Themajor non-ascomycete fungi were associated only with the class Exobasidiomycetes(Basidiomycota).At the order level,the epiphytes showed similar distribution patterns in the stems and leaves,but among the endophytes,distinct fungal orders were enriched in different tissues.Capnodialeswas recorded as amajor fungal group in the stems,leaves and seeds,and Saccharomycetales was specifically enriched in the pericarp and jelly around seeds.The present data suggested that different drivers shaped epiphytic and endophytic fungi communities and deepened our knowledge of the complex plant-fungus interaction in tomato. 展开更多
关键词 TOMATO Solanum lycopersicum ENDOPHYTIC epiphytic FUNGI Illumina sequencing
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基于重测序的芥蓝(Brassica alboglabra)全基因组InDel标记开发 认领
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作者 洪晓如 吴智明 +3 位作者 陈汉才 黎庭耀 沈卓 张艳 《分子植物育种》 CAS 北大核心 2021年第4期1190-1201,共12页
碱基插入/缺失(InDel)在基因组中的分布密度仅次于SNP且易于基因型分型,成为分子标记开发的主要来源。为了开发芥蓝品种间有多态性的分子标记,本研究利用2份芥蓝自交系重测序数据鉴定的InDel位点,在全基因组范围内设计了367对InDel候选... 碱基插入/缺失(InDel)在基因组中的分布密度仅次于SNP且易于基因型分型,成为分子标记开发的主要来源。为了开发芥蓝品种间有多态性的分子标记,本研究利用2份芥蓝自交系重测序数据鉴定的InDel位点,在全基因组范围内设计了367对InDel候选标记。通过PCR检测比较8个芥蓝自交系的多态性,发现284对标记在至少2个芥蓝自交系间有多态性,阳性率为77.4%。本研究利用重测序技术开发芥蓝品种间InDel标记效率较高,为种质资源分析、基因定位、分子标记辅助育种等提供了便捷工具。 展开更多
关键词 芥蓝(Brassica alboglabra) 重测序 INDEL标记
哺乳动物Y染色体的测序进展 认领
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作者 滑留帅 王璟 +3 位作者 汪聪勇 师志海 施巧婷 王二耀 《中国草食动物科学》 CAS 2021年第2期49-54,共6页
哺乳动物的性染色体由一对常染色体演化而来,其中X染色体在物种间相对保守,而Y染色体则存在很大的变异,包括染色体的大小、结构和基因数量等。研究Y染色体的遗传结构与变异,对于理解哺乳动物的起源进化、性别决定以及动物繁殖都具有重... 哺乳动物的性染色体由一对常染色体演化而来,其中X染色体在物种间相对保守,而Y染色体则存在很大的变异,包括染色体的大小、结构和基因数量等。研究Y染色体的遗传结构与变异,对于理解哺乳动物的起源进化、性别决定以及动物繁殖都具有重要意义。因此,文章综述了哺乳动物Y染色体的结构与变异,以及Sanger测序技术、二代测序技术、三代测序技术在Y染色体测序中的应用,并展望了基于CRISPR-dCas9可视化系统的流式染色体分离技术,以及高精度的三代测序技术在Y染色体测序中的应用前景。 展开更多
关键词 Y染色体 测序 CRISPR-dCas9 PacBio CCS
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