Specific Levels of DNA Methylation in Various Tissues, Cell Lines, and Cell Types of Daucus carota

The level of DNA methylation in Daucus carota was found to be tissue specific, but no simple correlation between developmental stage or age of tissue and the level of DNA methylation was found. Among three different suspension culture lines from the same variety grown under identical conditions, large differences in the level of DNA methylation were observed. The highest and lowest levels were found in two embryogenic cell lines originating from the same clone. Suspension cells from one of the embryogenic cell lines were fractionated into three morphologically defined cell types using Percoll gradient density centrifugation, and the uniformity of these fractions was evaluated by image analysis. The three cell types showed different levels of DNA methylation. The lowest level was found in the fraction containing the precursor cells of somatic embryos.     

Comparative Study of Seven Commercial Kits for Human DNA Extraction from Urine Samples Suitable for DNA Biomarker-Based Public Health Studies

Human genomic DNA extracted from urine could be an interesting tool for large-scale public health studies involving characterization of genetic variations or DNA biomarkers as a result of the simple and noninvasive collection method. These studies, involving many samples, require a rapid, easy, and standardized extraction protocol. Moreover, for practicability, there is a necessity to collect urine at a moment different from the first void and to store it appropriately until analysis. The present study compared seven commercial kits to select the most appropriate urinary human DNA extraction procedure for epidemiological studies. DNA yield has been determined using different quantification methods: two classical, i.e., NanoDrop and PicoGreen, and two species-specific real-time quantitative (q)PCR assays, as DNA extracted from urine contains, besides human, microbial DNA also, which largely contributes to the total DNA yield. In addition, the kits giving a good yield were also tested for the presence of PCR inhibitors. Further comparisons were performed regarding the sampling time and the storage conditions. Finally, as a proof-of-concept, an important gene related to smoking has been genotyped using the developed tools. We could select one well-performing kit for the human DNA extraction from urine suitable for molecular diagnostic real-time qPCR-based assays targeting genetic variations, applicable to large-scale studies. In addition, successful genotyping was possible using DNA extracted from urine stored at −20°C for several months, and an acceptable yield could also be obtained from urine collected at different moments during the day, which is particularly important for public health studies.     

Hypomethylation of Serum Blood Clot DNA,but Not Plasma EDTA-Blood Cell Pellet DNA,from Vitamin B12-Deficient Subjects

Vitamin B12, a co-factor in methyl-group transfer, is important in maintaining DNA (deoxycytidine) methylation. Using two independent assays we examined the effect of vitamin B12-deficiency (plasma vitamin B12<148 pmol/L) on DNA methylation in women of childbearing age. Coagulated blood clot DNA from vitamin B12-deficient women had significantly (p<0.001) lower percentage deoxycytidine methylation (3.23±0.66%; n = 248) and greater [3 H]methyl-acceptance (42,859±9,699 cpm; n = 17) than DNA from B12-replete women (4.44±0.18%; n = 128 and 26,049±2,814 cpm; n = 11) [correlation between assays: r = –0.8538; p<0.001; n = 28]. In contrast, uncoagulated EDTA-blood cell pellet DNA from vitamin B12-deficient and B12-replete women exhibited similar percentage methylation (4.45±0.15%; n = 77 vs. 4.47±0.15%; n = 47) and [3 H]methyl-acceptance (27,378±4,094 cpm; n = 17 vs. 26,610±2,292 cpm; n = 11). Therefore, in simultaneously collected paired blood samples, vitamin B12-deficiency was associated with decreased DNA methylation only in coagulated samples. These findings highlight the importance of sample collection methods in epigenetic studies, and the potential impact biological processes can have on DNA methylation during collection.     

A Practical and Novel Method to Extract Genomic DNA from Blood Collection Kits for Plasma Protein Preservation

Laboratory tests can be done on the cellular or fluid portions of the blood. The use of different blood collection tubes determines the portion of the blood that can be analyzed (whole blood, plasma or serum). Laboratories involved in studying the genetic basis of human disorders rely on anticoagulated whole blood collected in EDTA-containing vacutainer as the source of DNA for genetic / genomic analysis. Because most clinical laboratories perform biochemical, serologic and viral testing as a first step in phenotypic outcome investigation, anticoagulated blood is also collected in heparin-containing tube (plasma tube). Therefore when DNA and plasma are needed for simultaneous and parallel analyses of both genomic and proteomic data, it is customary to collect blood in both EDTA and heparin tubes. If blood could be collected in a single tube and serve as a source for both plasma and DNA, that method would be considered an advancement to existing methods. The use of the compacted blood after plasma extraction represents an alternative source for genomic DNA, thus minimizing the amount of blood samples processed and reducing the number of samples required from each patient. This would ultimately save time and resources.The BD P100 blood collection system for plasma protein preservation were created as an improved method over previous plasma or serum collection tubes¹, to stabilize the protein content of blood, enabling better protein biomarker discovery and proteomics experimentation from human blood. The BD P100 tubes contain 15.8 ml of spray-dried K2EDTA and a lyophilized proprietary broad spectrum cocktail of protease inhibitors to prevent coagulation and stabilize the plasma proteins. They also include a mechanical separator, which provides a physical barrier between plasma and cell pellets after centrifugation. Few methods have been devised to extract DNA from clotted blood samples collected in old plasma tubes^2-4. Challenges from these methods were mainly associated with the type of separator inside the tubes (gel separator) and included difficulty in recovering the clotted blood, the inconvenience of fragmenting or dispersing the clot, and obstruction of the clot extraction by the separation gel.We present the first method that extracts and purifies genomic DNA from blood drawn in the new BD P100 tubes. We compare the quality of the DNA sample from P100 tubes to that from EDTA tubes. Our approach is simple and efficient. It involves four major steps as follows: 1) the use of a plasma BD P100 (BD Diagnostics, Sparks, MD, USA) tube with mechanical separator for blood collection, 2) the removal of the mechanical separator using a combination of sucrose and a sterile paperclip metallic hook, 3) the separation of the buffy coat layer containing the white cells and 4) the isolation of the genomic DNA from the buffy coat using a regular commercial DNA extraction kit or a similar standard protocol.     

hSef基因在不同人组织和细胞系的表达分布

将人源Sef蛋白胞内区编码序列与GST融合构建原核表达质粒进行重组蛋白的表达与纯化并制备多抗 .在COS 7细胞中转染表达hSef显示 ,其分子量分别为 80kD ,10 0kD ,比体外翻译的分子量偏大 ,提示可能有糖基化存在 .Northern印迹的结果表明 ,hSefmRNA主要分布在人肾和睾丸组织 .RT PCR检测到hSefmRNA在众多细胞系有广泛存在 .免疫组化的结果显示 ,hSef蛋白在人肾和睾丸及相应癌组织表达水平较高 .     

施氏鲟不同组织来源细胞离体培养的初步研究

采用组织块移植培养技术,对来源于施氏鲟(Amursturgeon,Acipenser schrencki Brandt)肝脏、脾脏、肾脏、鳍条和心脏组织的细胞进行了原代培养,2～3天左右可见组织块周围有成纤维样细胞迁出,10天左右组织块周围形成单层细胞。对原代培养的单层细胞用胰蛋白酶-EDTA消化后传代培养,建立了可连续传代的施氏鲟肝脏、脾脏、肾脏、心脏组织细胞系。初步确立施氏鲟细胞培养的条件,培养基为MEME,培养温度为25℃,血清浓度为20%。对传代培养细胞以二甲基亚砜为保护剂在液氮冷冻保存,细胞复苏后可连续传代培养。施氏鲟细胞离体培养为开展鲟鱼病毒病和遗传资源保存研究提供了重要试验材料。     

A streamlined method for analysing genome-wide DNA methylation patterns from low amounts of FFPE DNA

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.

     

PCR-Free Enrichment of Mitochondrial DNA from Human Blood and Cell Lines for High Quality Next-Generation DNA Sequencing

Recent advances in sequencing technology allow for accurate detection of mitochondrial sequence variants, even those in low abundance at heteroplasmic sites. Considerable sequencing cost savings can be achieved by enriching samples for mitochondrial (relative to nuclear) DNA. Reduction in nuclear DNA (nDNA) content can also help to avoid false positive variants resulting from nuclear mitochondrial sequences (numts). We isolate intact mitochondrial organelles from both human cell lines and blood components using two separate methods: a magnetic bead binding protocol and differential centrifugation. DNA is extracted and further enriched for mitochondrial DNA (mtDNA) by an enzyme digest. Only 1 ng of the purified DNA is necessary for library preparation and next generation sequence (NGS) analysis. Enrichment methods are assessed and compared using mtDNA (versus nDNA) content as a metric, measured by using real-time quantitative PCR and NGS read analysis. Among the various strategies examined, the optimal is differential centrifugation isolation followed by exonuclease digest. This strategy yields >35% mtDNA reads in blood and cell lines, which corresponds to hundreds-fold enrichment over baseline. The strategy also avoids false variant calls that, as we show, can be induced by the long-range PCR approaches that are the current standard in enrichment procedures. This optimization procedure allows mtDNA enrichment for efficient and accurate massively parallel sequencing, enabling NGS from samples with small amounts of starting material. This will decrease costs by increasing the number of samples that may be multiplexed, ultimately facilitating efforts to better understand mitochondria-related diseases.     

Potential Small Guide RNAs for tRNase ZL from Human Plasma,Peripheral Blood Mononuclear Cells,and Cultured Cell Lines

Several pieces of evidence suggest that small RNA degradation products together with tRNase Z^L appear to form another layer of the whole gene regulatory network. The degraded RNA such as a 5′-half-tRNA and an rRNA fragment function as small guide RNA (sgRNA) to guide the enzyme to target RNA. We were curious whether there exist RNAs in plasma that can function as sgRNAs for tRNase Z^L, whether these RNAs are working as signaling molecules between cells to fulfill physiological roles, and whether there are any differences in plasma sgRNA species and levels between normal and pathological conditions. Here, we analyzed small plasma RNAs from three healthy persons and three multiple myeloma patients for potential sgRNAs by deep sequencing. We also examined small RNAs from peripheral blood mononuclear cells (PBMC) of three healthy persons and three myeloma patients and from various cultured human cell lines for sgRNAs. We found that read-number distribution patterns of plasma and PBMC RNAs differ between persons in the range of 5–40 nt and that there are many RNA species that exist significantly more or less abundantly in the plasma or PBMC of the myeloma patients than those of the healthy persons. Furthermore, we found that there are many potential sgRNAs in the 5–40-nt RNAs and that, among them, a 31-nt RNA fragment derived from 94-nt Y4-RNA, which can function as a 5′-half-tRNA-type sgRNA, is overwhelmingly abundant in the plasma of 2/3 of the examinees. These observations suggest that the gene regulatory network via tRNase Z^L and sgRNA may be extended intercellularly.     

Systematic Cross-biospecimen Evaluation of DNA Extraction Kits for Long- and Short-read Multi-metagenomic Sequencing Studies

High-quality DNA extraction is a crucial step in metagenomic studies. Bias by different isolation kits impairs the comparison across datasets. A trending topic is, however, the analysis of multiple metagenomes from the same patients to draw a holistic picture of microbiota associated with diseases. We thus collected bile, stool, saliva, plaque, sputum, and conjunctival swab samples and performed DNA extraction with three commercial kits. For each combination of the specimen type and DNA extraction kit, 20-gigabase (Gb) metagenomic data were generated using short-read sequencing. While profiles of the specimen types showed close proximity to each other, we observed notable differences in the alpha diversity and composition of the microbiota depending on the DNA extraction kits. No kit outperformed all selected kits on every specimen. We reached consistently good results using the Qiagen QiAamp DNA Microbiome Kit. Depending on the specimen, our data indicate that over 10 Gb of sequencing data are required to achieve sufficient resolution, but DNA-based identification is superior to identification by mass spectrometry. Finally, long-read nanopore sequencing confirmed the results (correlation coefficient > 0.98). Our results thus suggest using a strategy with only one kit for studies aiming for a direct comparison of multiple microbiotas from the same patients.     

一种新的与细胞分化相关的基因在不同组织及细胞系中表达与定位

目的　研究一种新的可能与细胞分化相关的基因在正常组织、肿瘤组织及细胞系中的表达与定位 ,初步探讨该基因的作用机制。方法　利用Northern杂交方法检测 10种人胎儿组织、6种人肿瘤细胞系、4种人的肿瘤组织及癌旁组织中该基因的表达。利用免疫荧光实验检测该基因在细胞中定位。结果　该基因在人的胎儿组织及肿瘤组织和肿瘤细胞中均有高表达 ,在正常组织及癌旁组织中表达明显减弱。癌旁组织和癌组织中的表达差异有显著性 (P <0 0 5 )。该基因在K56 2 细胞中主要定位在膜上。结论　该基因可能在细胞分化及肿瘤发生中起着重要作用     

Comparison of Plasma and Urine Biomarker Performance in Acute Kidney Injury

Background

New renal biomarkers measured in urine promise to increase specificity for risk stratification and early diagnosis of acute kidney injury (AKI) but concomitantly may be altered by urine concentration effects and chronic renal insufficiency. This study therefore directly compared the performance of AKI biomarkers in urine and plasma.

Methods

This single-center, prospective cohort study included 110 unselected adults undergoing cardiac surgery with cardiopulmonary bypass between 2009 and 2010. Plasma and/or urine concentrations of creatinine, cystatin C, neutrophil gelatinase-associated lipocalin (NGAL), liver fatty acid-binding protein (L-FABP), kidney injury molecule 1 (KIM1), and albumin as well as 15 additional biomarkers in plasma and urine were measured during the perioperative period. The primary outcome was AKI defined by AKIN serum creatinine criteria within 72 hours after surgery.

Results

Biomarkers in plasma showed markedly better discriminative performance for preoperative risk stratification and early postoperative (within 24h after surgery) detection of AKI than urine biomarkers. Discriminative power of urine biomarkers improved when concentrations were normalized to urinary creatinine, but urine biomarkers had still lower AUC values than plasma biomarkers. Best diagnostic performance 4h after surgery had plasma NGAL (AUC 0.83), cystatin C (0.76), MIG (0.74), and L-FAPB (0.73). Combinations of multiple biomarkers did not improve their diagnostic power. Preoperative clinical scoring systems (EuroSCORE and Cleveland Clinic Foundation Score) predicted the risk for AKI (AUC 0.76 and 0.71) and were not inferior to biomarkers. Preexisting chronic kidney disease limited the diagnostic performance of both plasma and urine biomarkers.

Conclusions

In our cohort plasma biomarkers had higher discriminative power for risk stratification and early diagnosis of AKI than urine biomarkers. For preoperative risk stratification of AKI clinical models showed similar discriminative performance to biomarkers. The discriminative performance of both plasma and urine biomarkers was reduced by preexisting chronic kidney disease.     

不同分化程度的鼻咽癌细胞系质膜差异蛋白质组分析

本研究以CNE1和CNE2为材料,采用亚细胞蛋白质组研究方法研究不同分化程度鼻咽癌细胞系的差异蛋白质．首先用Percoll密度梯度离心法获得高纯度质膜,通过双向凝胶电泳分离、PDQuest软件分析后找出在肿瘤细胞中表达变化的蛋白质点,再用基质辅助激光解析电离飞行时间串联质谱（MALDI-TOF/TOF-MS）进行鉴定,共鉴定到9个具有2倍或2倍以上差异的蛋白质.这些表达差异的蛋白质参与了细胞分化、代谢及细胞信号传导过程．我们对其中5个蛋白质进行了实时定量PCR分析,对其中4个蛋白质的表达进行了免疫印迹验证．本试验为研究不同分化程度的鼻咽癌提供了一种蛋白质组研究方法,并且找到了galectin-1、annexin Ⅱ等一些可能与分化相关的蛋白质.这些数据对于研究鼻咽癌的生物学特性具有非常重要的意义．     

A Two-Step Procedure for Quantitative Isolation of Pure Double Strand DNA from Animal Tissues and Cell Cultures

A two step procedure for the quantitative isolation of protein- and RNA-free double-strand DNA from animal tissue and cell homogenates is described. In the first step proteins not complexed with DNA are hydrolyzed with an immobilized protease (Proteinase K) that is separated by filtration after the de-proteinization. Then the DNA is adsorbed to hydroxylapatite (HA) and desorbed from the adsorbent by stepwise elution with buffers of increasing ionic strength. The DNA content was determined directly from the absorption at 260 nm. The melting curve of the isolated DNA showed that it was double stranded. The protein content in the DNA was determined from the ratio of the adsorbance at 260 to 230 nm. Non-histone proteins complexed to DNA determined the rate of deproteinization that was found to be tissue specific. These proteins were found to have a larger influence on the ratio A₂₆₀/A₂₃₀ than histones, indicating that their absorption (at 230 nm) is markedly perturbed when they are bound to DNA.     

HMGB1在胃癌组织及细胞系中表达的研究

目的:近年来的研究表明,高迁移率族蛋白(1HMGB1)在肿瘤的发生及恶性演变过程中发挥重要作用,本研究旨在探讨HMGB1在胃癌组织、正常组织、胃癌细胞系SGC-7901、BGC-823、HGC-27、AGS及正常胃黏膜细胞系GES中表达情况。方法:免疫组织化学法检测HMGB1在32例可手术切除的胃癌患者组织标本(包括癌组织和正常组织)的表达情况;RT-PCR及Westren Blot检测HMGB1在胃癌细胞系SGC-7901、BGC-823、HGC-27、AGS及正常胃粘膜细胞系GES的m RNA及蛋白质表达。结果:胃癌组织HMGB1免疫组织化学染色评分高于正常组织(P0.05);RT-PCR结果显示SGC-7901、BGC-823、HGC-27、AGS、GES细胞系HMGB1 m RNA表达丰度均较高;Westren Blot检测发现胃癌细胞系SGC-7901、BGC-823、HGC-27中HMGB1蛋白水平显著高于胃癌细胞系AGS及正常胃粘膜细胞系GES。结论:HMGB1在胃癌组织及正常组织中的表达具有显著性差异。胃癌细胞系SGC-7901、BGC-823、HGC-27相对于其它胃细胞系存在HMGB1高表达,适合后续基因敲除分析工作。     

肝癌组织及细胞系总RNA抽提逆转及基因克隆方法的改进与比较

本文建立了高效肝组织及细胞总RNA抽提、反转录以进行基因克隆和实时定量PCR（q-RT-PCR）的方法。 比较了2种反转录酶(M-MLV和SuperScriptII)、2种cDNA合成引物(Oligo dT和random 6 primer)对总RNA反转录效率的影响,与4种DNA聚合酶（Taq聚合酶、Pfu聚合酶、LA taq聚合酶、Prime Star聚合酶）进行长片段基因克隆的能力及效率;同时,该研究比较了不同质量总RNA对有效进行q-RT-PCR与长片段分子克隆的影响。新建立的RNA提取方法使得RNA完整性和均一性提高。RNA的完整性及均一性对长片段cDNA的克隆至关重要。部分降解的组织RNA及细胞RNA仅适合于q-RT-PCR检测mRNA的表达水平,而不适合于cDNA的克隆。