共查询到20条相似文献,搜索用时 46 毫秒
1.
Lei Jia Fengyu Hu Hanping Li Lin Li Xiaoping Tang Yongjian Liu Haohui Deng Jingwan Han Jingyun Li Weiping Cai 《Virology journal》2018,15(1):188
Background
Hepatitis B virus is a hepatotropic DNA virus that reproduces via an RNA intermediate. It can lead to an increased risk of serious liver diseases such as hepatocellular carcinoma and is a serious threat to public health. Currently, the HBV are designated based on greater than 8% nucleotide variation along the whole genome. The recombination of HBV is very common, a large majority of which are recombinants between 2 genotypes. The current work aims to characterize a suspected recombinant involving 3 genotypes.Methods
Fifty-seven HBV full-genome sequences were obtained from 57 patients co-infected with HBV and HIV-1 by amplification coupled with sequencing. JpHMM and RDP4 were used to perform recombination analysis respectively. The recombination results of a suspected 3-genotypic recombinant were further confirmed by both maximum likelihood phylogenetic tree and Mrbayes tree.Results
JpHMM recombination analysis clearly indicated one 3-genotypic HBV recombinant composing of B/C/D. The genotype assignments are supported by significant posterior probabilities. The subsequent phylogenetic analysis of sub-regions derived from inferred breakpoints led to a disagreement on the assignment of D segment. Investigating the conflict, further exploration by RDP4 and phylogenies revealed that the jpHMM-derived 3-genotypic recombinant is actually a B/C genotypic recombinant with C fragment spanning 1899 to 2295 (jpHMM) or 1821 to 2199 (RDP4).Conclusions
The whole analysis indicated that (i) determination of small genomic regions should be performed with more caution, (ii) combinations of various recombination detection approaches conduce to obtain impartial results, and (iii) a unified system of nomenclature of HBV genotypes is necessary.2.
3.
Deuk-Ju Lee Jong-Dae Kim Yu-Seop Kim Hye-Jeong Song Chan-Young Park 《Biomedical engineering online》2018,17(2):150
Background
In general, the image analysis of nucleic acid for detecting DNA is dependent on the gel documentation system. These experiments may deal with harmful staining agents and are time consuming. To address these issues, real-time polymerase chain reaction (PCR) devices have been developed. The advantages of real-time PCR are its capabilities for real-time diagnosis, improved sensitivity, and digitization of measurement results. However, real-time PCR equipment is still too bulky and expensive for use in small hospitals and laboratories.Methods
This paper describes an evaluation-independent real-time PCR system that differs from conventional systems in that it uses a side-illumination optical detection system and a temperature adjustment coefficient for DNA detection. The overall configuration of the evaluation-independent system includes the PCR chip and system hardware and software. The use of the side-illumination method for detection enables the system size to be reduced compared to systems using a typical illumination method. Furthermore, the results of a PCR test are strongly affected by the reaction temperature. Thus, extremely precise control of the temperature of the reaction is needed to obtain accurate results and good reliability. We derived a temperature compensation coefficient that allows us to compensate for the differences between the measured temperature of the negative temperature coefficient (NTC) thermistor sensor and the real temperature of the thermocouple.Results
Applying the temperature compensation coefficient parameter using the NTC thermistor and using the side-illumination method resulted in an increase in the initial sensor value. The occurrence of the DNA section amplification decreased to 22 cycles from 24 cycles.Conclusions
The proposed system showed comparable performance to that of an existing real-time PCR, even with the use of simpler and smaller optical devices.4.
Rachel A. Spicer Christoph Steinbeck 《Metabolomics : Official journal of the Metabolomic Society》2018,14(1):16
Introduction
Data sharing is being increasingly required by journals and has been heralded as a solution to the ‘replication crisis’.Objectives
(i) Review data sharing policies of journals publishing the most metabolomics papers associated with open data and (ii) compare these journals’ policies to those that publish the most metabolomics papers.Methods
A PubMed search was used to identify metabolomics papers. Metabolomics data repositories were manually searched for linked publications.Results
Journals that support data sharing are not necessarily those with the most papers associated to open metabolomics data.Conclusion
Further efforts are required to improve data sharing in metabolomics.5.
Yang Chen Wanzhu Guo Zhiwen Xu Qigui Yan Yan Luo Qian Shi Dishi Chen Ling Zhu Xiaoyu Wang 《Virology journal》2011,8(1):307
Background
Porcine parvovirus (PPV) VP2 gene has been successfully expressed in many expression systems resulting in self-assembly of virus-like particles (VLPs) with similar morphology to the native capsid. Here, a pseudorabies virus (PRV) system was adopted to express the PPV VP2 gene.Methods
A recombinant PRV SA215/VP2 was obtained by homologous recombination between the vector PRV viral DNA and a transfer plasmid. Then recombinant virus was purified with plaque purification, and its identity confirmed by PCR amplification, Western blot and indirect immunofluorescence (IFA) analyses. Electronic microscopy of PRV SA215/VP2 confirmed self-assembly of both pseudorabies virus and VLPs from VP2 protein.Results
Immunization of piglets with recombinant virus elicited PRV-specific and PPV-specific humoral immune responses and provided complete protection against a lethal dose of PRV challenges. Gilts immunized with recombinant viruses induced PPV-specific antibodies, and significantly reduced the mortality rate of (1 of 28) following virulent PPV challenge compared with the control (7 of 31). Furthermore, PPV virus DNA was not detected in the fetuses of recombinant virus immunized gilts.Conclusions
In this study, a recombinant PRV SA215/VP2 virus expressing PPV VP2 protein was constructed using PRV SA215 vector. The safety, immunogenicity, and protective efficacy of the recombinant virus were demonstrated in piglets and primiparous gilts. This recombinant PRV SA215/VP2 represents a suitable candidate for the development of a bivalent vaccine against both PRV and PPV infection.6.
Xiao-Feng Wang Wen-Yu Wu Gao-Kun Qiu Hao Wang Wen-Si Li Yong-Li Wang Qun-Qun Jiang Mei-Fang Han Qin Ning 《Metabolomics : Official journal of the Metabolomic Society》2017,13(6):76
Introduction
Acute-on-chronic liver failure (ACLF) is a fatal syndrome that presents with acute deterioration of liver function in chronic hepatitis B virus (HBV) patients. However, reliable diagnostic and prognostic biomarkers are scarce.Objectives
The aim of this study to identify lipid species associated with HBV infection as well as novel lipid biomarkers for HBV-ACLF.Methods
High performance liquid chromatography–tandem mass spectrometry was used for targeted lipidomic analyses of 147 lipid species. Fasting-state plasma samples from 74 HBV-ACLF patients, 86 HBV-non-ACLF patients [30 HBV-immune tolerant (HBV-IT) and 56 chronic hepatitis B] and 20 healthy controls. Univariate and multivariate analyses examined changes in lipid species among patient groups.Results
The HBV-ACLF and HBV-non-ACLF groups had distinctly different lipid profiles, while the HC and HBV-IT groups had similar lipid profiles. Further, lysophosphatidylcholine (LPC) 22:6, cholesterol ester (CE) 22:6, CE 20:4, CE 18:2 and CE 18:1 could be used as potential biomarkers for the early prediction of ACLF. Meanwhile, univariate and multivariate analyses identified CE 20:4, LPC 16:0, LPC 18:0, phosphatidylcholine (PC) 40:6 and PC 32:0 as putative diagnostic biomarkers of HBV-ACLF. Moreover, LPC 16:0 and LPC 18:0 were significantly associated with model for end stage liver disease (MELD) scores, and the two lipid species combined with MELD score had significant capability to predict the 6-month mortality.Conclusions
Our study revealed that lipid metabolism disorders were significantly associated with the severity of liver inflammatory injury rather than HBV infection in patients with chronic HBV infection, and specific lipid species could be used as potentially biomarkers for diagnosis and prognosis in HBV-ACLF.7.
Mostafa Paridar Abbas Khosravi Mohammad-Ali Jalali-Far Sima Zolfaghari Omid Kiani Ghaleh Sardi Mehdi Sajadi 《生物学前沿》2018,13(3):226-234
Background
The determination of the role of mobile sites, as compared with fixed sites, in providing safe blood supply will help with the planning of future programs.Materials and Methods
This retrospective study was carried out at the Khuzestan Blood Transfusion Organization from 2007 to 2012. Samples of the blood collected at mobile sites and fixed sites were compared. Comparisons took into consideration noticeable trends as well as the prevalence of major TTIs including HIV, HBV and HCV.Results
The total number of blood donations from 2007 to 2012 was 621117 out of which 89590 (14.43%) were collected from mobile sites. The overall blood donation index was estimated at 23.8 per 1000 population. The prevalence of HIV, HBV and HCV in mobile site donations was 5.31, 320.34 and 117.4, and in fixed sites was 5.31, 214.72 and 104.83 per 100000 donations respectively. HBV prevalence in mobile sites was significantly higher than in fixed sites (p = 0.014).Conclusion
The blood donation index in Khuzestan province is much better when compared with areas of similar socioeconomic status as well as neighboring countries. The allotment of blood units collected by mobile teams is lower than that of national reports. In addition, the prevalence of TTIs in mobile site blood donations was higher than at fixed sites.8.
Hong Zheng Minjiang Chen Siming Lu Liangcai Zhao Jiansong Ji Hongchang Gao 《Metabolomics : Official journal of the Metabolomic Society》2017,13(10):121
Introduction
Liver cirrhosis (LC) is an advanced liver disease that can develop into hepatocellular carcinoma. Hepatitis B virus (HBV) infection is one of the main causes of LC. Therefore, there is an urgent need for developing a new method to monitor the progression of HBV-related LC (HBV-LC).Objectives
In this study, we attempted to examine serum metabolic changes in healthy individuals as well as patients with HBV and HBV-LC. Furthermore, potential metabolite biomarkers were identified to evaluate patients progressed from health to HBV-LC.Methods
Metabolic profiles in the serum of healthy individuals as well as patients with HBV and HBV-LC were detected using an NMR-based metabolomic approach. Univariate and multivariate analyses were conducted to analyze serum metabolic changes during HBV-LC progression. Moreover, potential metabolite biomarkers were explored by receiver operating characteristic curve analysis.Results
Serum metabolic changes were closely associated with the progression of HBV-LC, mainly involving energy metabolism, protein metabolism, lipid metabolism and microbial metabolism. Serum histidine was identified as a potential biomarker for HBV patients. Acetate, formate, pyruvate and glutamine in the serum were identified as a potential biomarker panel for patients progressed from HBV to HBV-LC. In addition, phenylalanine, unsaturated lipid, n-acetylglycoprotein and acetone in the serum could be considered as a potential common biomarkers panel for these patients.Conclusion
NMR-based serum metabolomic approach could be a promising tool to monitor the progression of liver disease. Different metabolites may reflect different stages of liver disease.9.
Yahya Mohammadzadeh Narges Rasouli Mohammad Hasan Samiee Aref Nasim Sadat Seyed Tabib Asghar Abdoli Peyvand Biglari Maryam Saleh Mansoureh Tabatabaeian Masoumeh Tavassoti Kheiri Abbas Jamali 《Biotechnology letters》2016,38(8):1321-1329
Objectives
To enhance the efficiency of influenza virosome-mediated gene delivery by engineering this virosome.Results
A novel chimeric influenza virosome was constructed containing the glycoprotein of Vesicular stomatitis virus (VSV-G), along with its own hemagglutinin protein. To optimize the transfection efficiency of both chimeric and influenza cationic virosomes, HEK cells were transfected with plasmid DNA and virosomes and the transfection efficiency was assessed by FACS analysis. The chimeric virosome was significantly more efficient in mediating transfection for all amounts of DNA and virosomes compared to the influenza virosome.Conclusions
Chimeric influenza virosome, including VSV-G, is superior to the conventional influenza virosome for gene delivery.10.
Background
Xenotransplantation has drawn increased attention in recent years as a potential solution to the scarcity of human source donor organs. Researchers have highlighted the need to characterize the influence of porcine endogenous retroviruses (PERV) in xenotransplantation. Screening and analyzing the presence and subtype of PERV in donor source animal breeds could provide basic parameters to evaluate the biological safety of xenotransplantation from pigs to humans. We bred a new miniature porcine herd (XENO-1) after decades of investigation, the herd was purpose bred to produce a potential donor animal source for xenotransplantation. To this end we studied the animals’ PERV expression characteristics.Methods
We randomly selected 37 animals of the herd, PCR and RT-PCR based on specific primers were utilized to determine their PERV viral subtype. High fidelity PCR and restriction enzyme digestion were employed for variants detection. To thoroughly understand the PERV expression pattern, quantitative PCR was applied to measure mRNA expression levels in different tissues, At last, transfection capacity was assessed using a in vitro co-culture system.Results
Our results revealed that the XENO-1 herd was free of PERV-C and exhibited low levels of PERVs in different tissues compared to commercial pig (landrace). The XENO-1 herd showed unique variants of A/B recombination. In addition, even though there were A/B variants in the XENO-1 herd, co-culturing revealed no evidence of PERV transmission from XENO-1 tissue to human cells.Conclusion
Overall, Our results displayed an unique PERV expression pattern in a new pig herd and demonstrated its non-transfection capacity in vitro. Data in the research indicate that XENO-1 animals can serve as a better potential donor source for xenotransplantation.11.
Nadine Strehmel David Strunk Veronika Strehmel 《Metabolomics : Official journal of the Metabolomic Society》2017,13(11):135
Introduction
Aqueous–methanol mixtures have successfully been applied to extract a broad range of metabolites from plant tissue. However, a certain amount of material remains insoluble.Objectives
To enlarge the metabolic compendium, two ionic liquids were selected to extract the methanol insoluble part of trunk from Betula pendula.Methods
The extracted compounds were analyzed by LC/MS and GC/MS.Results
The results show that 1-butyl-3-methylimidazolium acetate (IL-Ac) predominantly resulted in fatty acids, whereas 1-ethyl-3-methylimidazolium tosylate (IL-Tos) mostly yielded phenolic structures. Interestingly, bark yielded more ionic liquid soluble metabolites compared to interior wood.Conclusion
From this one can conclude that the application of ionic liquids may expand the metabolic snapshot.12.
13.
Background
Microsatellites are nucleotide sequences of tandem repeats occurring throughout the genome, which have been widely used in genetic linkage analysis, studies of loss of heterozygosity, determination of lineage and clonality, and the measurement of genome instability or the emergence of drug resistance reflective of mismatch repair deficiency. Such analyses may involve the parallel evaluation of many microsatellite loci, which are often limited by sample DNA, are labor intensive, and require large data processing.Results
To overcome these challenges, we developed a cost-effective high-throughput approach of microsatellite analysis, in which the amplifications of microsatellites are performed in miniaturized, multiplexed polymerase chain reaction (PCR) adaptable to 96 or 384 well plates, and accurate automated allele identification has been optimized with a collective reference dataset of 5,508 alleles using the GeneMapper software.Conclusions
In this investigation, we have documented our experience with the optimization of multiplex PCR conditions and automated allele identification, and have generated a unique body of data that provide a starting point for a cost-effective, high-throughput process of microsatellite analysis using the studied markers.14.
Background
Chicken anemia virus (CAV) is the causative agent of chicken infectious anemia. CAV putative intergenotypic recombinants have been reported previously. This fact is based on the previous classification of CAV sequences into three genotypes. However, it is unknown whether intersubtype recombination occurs between the recently reported four CAV genotypes and five subtypes of genome sequences.Results
Phylogenetic analysis, together with a variety of computational recombination detection algorithms, was used to investigate CAV approximately full genomes. Statistically significant evidence of intersubtype recombination was detected in the parent-like and two putative CAV recombinant sequences. This event was shown to occur between CAV subgroup A1 and A2 sequences in the phylogenetic trees.Conclusions
We revealed that intersubtype recombination in CAV genome sequences played a role in generating genetic diversity within the natural population of CAV.15.
Detection of Leishmania infantum DNA in the non-parasitized lung of dogs with visceral leishmaniasis
Ricardo Goncalves Soraia Oliveira Silva Gregório Guilherme de Almeida Carolina Carvalho de Souza Wagner Luiz Tafuri M. Norma Melo 《BMC veterinary research》2018,14(1):403
Background
Despite the very low or absent parasitism in the lungs, the interstitial pneumonitis is a common lesion found in humans and dogs with visceral leishmaniasis. The lung is a neglected organ in the study of dogs and humans with visceral leishmaniasis, but interstitial pneumonitis represents an important lesion characterized by thickening of the alveolar septum due to fibrosis and inflammatory exudate, and its pathogenesis is still uncertain. In this study, the polymerase chain reaction (PCR) was used to detect Leishmania infantum in paraffin-embedded lung biopsies from naturally infected dogs from an endemic area in Minas Gerais State, Brazil; PCR was compared to histological and immunohistochemical techniques for detecting Leishmania.Results
Eighteen dogs in which leishmaniasis had been diagnosed by serological tests - indirect immunofluorescence assay (IFAT), enzyme-linked immunosorbent assay (ELISA) and complement fixation tests (CFT) - were classified as asymptomatic, oligosymptomatic or symptomatic. Nine of the 18 dogs studied had a positive PCR (50%) but parasites were not detected by histopathological and immunocytochemistry methods.Conclusions
These data indicate that PCR on DNA extracted from paraffin-embedded tissue is a valuable method for detecting Leishmania infantum parasites in lungs of naturally infected dogs, despite the apparent absence of parasites from standard HE (hematoxylin and eosin) stained slides and of labeled parasites from immunocytochemical preparations.16.
Background
Methylation analysis of cell-free DNA is a encouraging tool for tumor diagnosis, monitoring and prognosis. Sensitivity of methylation analysis is a very important matter due to the tiny amounts of cell-free DNA available in plasma. Most current methods of DNA methylation analysis are based on the difference of bisulfite-mediated deamination of cytosine between cytosine and 5-methylcytosine. However, the recovery of bisulfite-converted DNA based on current methods is very poor for the methylation analysis of cell-free DNA.Results
We optimized a rapid method for the crucial steps of bisulfite conversion with high recovery of cell-free DNA. A rapid deamination step and alkaline desulfonation was combined with the purification of DNA on a silica column. The conversion efficiency and recovery of bisulfite-treated DNA was investigated by the droplet digital PCR. The optimization of the reaction results in complete cytosine conversion in 30 min at 70 °C and about 65% of recovery of bisulfite-treated cell-free DNA, which is higher than current methods.Conclusions
The method allows high recovery from low levels of bisulfite-treated cell-free DNA, enhancing the analysis sensitivity of methylation detection from cell-free DNA.17.
Background
DNA sequence can be viewed as an unknown language with words as its functional units. Given that most sequence alignment algorithms such as the motif discovery algorithms depend on the quality of background information about sequences, it is necessary to develop an ab initio algorithm for extracting the “words” based only on the DNA sequences.Methods
We considered that non-uniform distribution and integrity were two important features of a word, based on which we developed an ab initio algorithm to extract “DNA words” that have potential functional meaning. A Kolmogorov-Smirnov test was used for consistency test of uniform distribution of DNA sequences, and the integrity was judged by the sequence and position alignment. Two random base sequences were adopted as negative control, and an English book was used as positive control to verify our algorithm. We applied our algorithm to the genomes of Saccharomyces cerevisiae and 10 strains of Escherichia coli to show the utility of the methods.Results
The results provide strong evidences that the algorithm is a promising tool for ab initio building a DNA dictionary.Conclusions
Our method provides a fast way for large scale screening of important DNA elements and offers potential insights into the understanding of a genome.18.
Cong Wang Xiaomin Chen Yuying Wu Hao Li Yu Wang Xiaofu Pan Tingting Tang Ziying Liu Xiaokun Li 《Biotechnology letters》2016,38(10):1709-1714
Objectives
To develop a convenient and sensitive point-of-care test for detecting gene mutations based on allele-specific PCR.Results
To develop a lateral flow strip for visual detection of K-ras mutations based on a modified PCR, a specific DNA tag was covalently linked to the 5′-end of each primer by a nine-carbon linker to produce a sticky end. One of the sticky ends of the PCR products bound to gold nano-particles, while the other sticky end was captured onto a nitrocellulose membrane of lateral flow strips. The lateral flow strip showed a great sensitivity, which detected mutations in as low as 10 tumor cells. The positive rate and accuracy of the lateral flow strip for blood samples were over 92 and 96 %, respectively.Conclusions
The lateral flow strip provides an easy method for sensitive detection of gene mutations based on allele specific-PCR.19.
A streamlined method for analysing genome-wide DNA methylation patterns from low amounts of FFPE DNA
Jackie L. Ludgate James Wright Peter A. Stockwell Ian M. Morison Michael R. Eccles Aniruddha Chatterjee 《BMC medical genomics》2017,10(1):54
Background
Formalin fixed paraffin embedded (FFPE) tumor samples are a major source of DNA from patients in cancer research. However, FFPE is a challenging material to work with due to macromolecular fragmentation and nucleic acid crosslinking. FFPE tissue particularly possesses challenges for methylation analysis and for preparing sequencing-based libraries relying on bisulfite conversion. Successful bisulfite conversion is a key requirement for sequencing-based methylation analysis.Methods
Here we describe a complete and streamlined workflow for preparing next generation sequencing libraries for methylation analysis from FFPE tissues. This includes, counting cells from FFPE blocks and extracting DNA from FFPE slides, testing bisulfite conversion efficiency with a polymerase chain reaction (PCR) based test, preparing reduced representation bisulfite sequencing libraries and massively parallel sequencing.Results
The main features and advantages of this protocol are:
- An optimized method for extracting good quality DNA from FFPE tissues.
- An efficient bisulfite conversion and next generation sequencing library preparation protocol that uses 50 ng DNA from FFPE tissue.
- Incorporation of a PCR-based test to assess bisulfite conversion efficiency prior to sequencing.
Conclusions
We provide a complete workflow and an integrated protocol for performing DNA methylation analysis at the genome-scale and we believe this will facilitate clinical epigenetic research that involves the use of FFPE tissue.20.
Jong-Dae Kim So-Yeon Lee Yu-Seop Kim Hye-Jeong Song Chan-Young Park 《Biomedical engineering online》2018,17(2):153