Implications of cancer-associated systemic inflammation for biomarker studies

Highly sensitive molecular technologies provide new capacities for cancer biomarker research, but with sensitivity improvements marker specificity is significantly decreased, and too many false-positive results should disqualify the measurement from clinical use. Hence, of the thousands of potential cancer biomarkers only a few have found their way to clinical application. Differentiating false-positive results from true-positive (cancer-specific) results can indeed be difficult, if validation of a marker is performed against inadequate controls.     

Time‐dependent classification accuracy curve under marker‐dependent sampling

Evaluating the classification accuracy of a candidate biomarker signaling the onset of disease or disease status is essential for medical decision making. A good biomarker would accurately identify the patients who are likely to progress or die at a particular time in the future or who are in urgent need for active treatments. To assess the performance of a candidate biomarker, the receiver operating characteristic (ROC) curve and the area under the ROC curve (AUC) are commonly used. In many cases, the standard simple random sampling (SRS) design used for biomarker validation studies is costly and inefficient. In order to improve the efficiency and reduce the cost of biomarker validation, marker‐dependent sampling (MDS) may be used. In a MDS design, the selection of patients to assess true survival time is dependent on the result of a biomarker assay. In this article, we introduce a nonparametric estimator for time‐dependent AUC under a MDS design. The consistency and the asymptotic normality of the proposed estimator is established. Simulation shows the unbiasedness of the proposed estimator and a significant efficiency gain of the MDS design over the SRS design.     

Global diversity and genetic contributions of chicken populations from African,Asian and European regions

Genetic diversity and population structure of 113 chicken populations from Africa, Asia and Europe were studied using 29 microsatellite markers. Among these, three populations of wild chickens and nine commercial purebreds were used as reference populations for comparison. Compared to commercial lines and chickens sampled from the European region, high mean numbers of alleles and a high degree of heterozygosity were found in Asian and African chickens as well as in Red Junglefowl. Population differentiation (F_ST) was higher among European breeds and commercial lines than among African, Asian and Red Junglefowl populations. Neighbour‐Net genetic clustering and structure analysis revealed two main groups of Asian and north‐west European breeds, whereas African populations overlap with other breeds from Eastern Europe and the Mediterranean region. Broilers and brown egg layers were situated between the Asian and north‐west European clusters. structure analysis confirmed a lower degree of population stratification in African and Asian chickens than in European breeds. High genetic differentiation and low genetic contributions to global diversity have been observed for single European breeds. Populations with low genetic variability have also shown a low genetic contribution to a core set of diversity in attaining maximum genetic variation present from the total populations. This may indicate that conservation measures in Europe should pay special attention to preserving as many single chicken breeds as possible to maintain maximum genetic diversity given that higher genetic variations come from differentiation between breeds.     

甘蓝型油菜花瓣缺失基因的图谱定位

在无花瓣品系APT02和正常有花瓣品种中双4号构建的的F2分离群体中,运用AFLP和SRAP两种标记技术对甘蓝型油菜花瓣缺失基因进行分子标记和图谱定位。在两亲本间筛选20对AFLP引物和170对SRAP 引物,进一步通过BSA法筛选,获得了与甘蓝型油菜花瓣缺失基因WHB连锁的1个SRAP标记e8m3_4（600bp）和1个AFLP标记E3247_15（150bp）,标记与基因WHB之间的遗传距离分别为5 cM和13.5cM;构建了一个甘蓝型油菜(Brassica napus.L )的分子标记遗传连锁图谱,该图谱共包含213个AFLP标记、56个SRAP标记和1个形态标记,分布于17个主要连锁群、两个三联体和4个连锁对中,遗传图距总长2487.1cM,标记间平均距离为10.09 cM。通过图谱定位,控制花瓣缺失性状的基因WHB被定位到第4连锁群(LG4)上。     

Alkaline phosphatase staining of pig and sheep epiblast cells in culture

To define better the characteristics of pig and sheep epiblast cells in culture, the cells were tested for the presence of alkaline phosphatase (AP), a biochemical marker characteristic of mouse embryonic stem cells. Pig and sheep epiblast cells were positive for AP staining both at isolation from the blastocyst and after primary in vitro culture. The innermost portion of the attendant endoderm surrounding the epiblast was also positive for AP staining during primary culture. AP staining was lost upon differentiation or senescence of the epiblast cells. Also, all differentiated epiblast-derived cell cultures were negative for AP staining, with the exception of neuron-like cultures. Epiblast-like cells were cultured from day 10 (pig) and day 13 (sheep) embryonic discs, and these cells were also AP positive until they differentiated. Trophectoderm-endoderm-like cells from embryonic discs were AP negative or weakly positive. AP is a convenient marker for undifferentiated pig and sheep epiblast cells in culture when used in conjunction with cell morphology analysis. © 1993 Wiley-Liss, Inc.     

水稻抗性基因定位及相关分子标记研究进展

水稻是一种重要的粮食作物。而选育高抗性良种是有效防治病虫的危害,增加水稻单位面积产量的一项关键措施。了解水稻本身抗性的遗传信息是进行抗性育种的基础。现代生物技术的发展为抗性育种提供了新途径。本文较系统地概述了水稻对稻瘟病、白叶枯病、稻飞虱、稻叶蝉抗性基因定位及相关分子标记研究的最新发展,为利用分子标记进行水稻抗性育种及抗性基因克隆提供参考文献。     

转基因植物生物安全标记基因

在大量转基因植物被推向市场的同时,人们对转基因植物对环境及人类健康等许多方面可能存在的风险感到担扰。标记基因的生物安全性成为人们普遍关注的问题之一。新的标记基因不仅要求能够对转基因植物进行筛选和鉴定,而且必须对环境和生物都是安全的。概述并评价了绿色荧光蛋白基因、核糖醇操纵子、6磷酸甘露糖异构酶基因、木糖异构酶基因以及谷氨酸1半醛转氨酶基因等生物安全标记基因及其最新研究进展 。     

应用RAPD标记检测导入普通小麦中的Elymus rectisetus遗传物质

以72个含16株系的BC2F5（小麦/Elymus rectisetus//小麦）单株为供体材料,用筛选出的12个10碱基随机引物对其进行多态性扩增。以E.rectisetus和Fukuhokomugi(Triticum aestivum)为亲本,建立RAPD标记。实验表明：12个随机引物中,有10个随机引物能够在16个株系的68个单株中分别扩增出普通小麦所没有的E.rectisetus的DNA片段,可分为6个类型,此外,1040-2-5-1和1048-Y3-3-1可能含5种异源染色体。     

小麦HMW-GS基因及其AS-PCR分子标记研究进展

小麦高分子量谷蛋白亚基(HMW-GS)与小麦品质性状,尤其是沉降值性状显著相关。利用其做分子标记选育聚合优质亚基的品种,具有快速、简单、实用、有效的特点。目前,普通小麦基因组中已有15个已命名Glu-1基因被克隆和测序,这使设计引物序列、进行等位基因的特异性扩增成为可能。对普通小麦高分子量谷蛋白亚基基因组成特点及分子标记现状进行了分析,并针对国内利用高分子量谷蛋白亚基进行分子标记辅助育种做了展望。     

微卫星标记及其在动物遗传育种中的应用

微卫星标记技术一出现,就以其独特的优点引起了动物遗传育种学家的广泛关注,显示出较好的应用前景。本文就微卫星标记的特点及其在动物遗传育种中的应用作以综述。     

血循环DNA在淋巴瘤中的研究进展

近年来血循环DNA用于基因诊断已成为研究热点,血循环DNA是指血浆中具有DNA双螺旋结构的核苷酸片段,逐渐成为一项新的肿瘤标记物。研究发现肿瘤患者血循环DNA较正常人有很大差异,不同疾病条件下其含量有不同程度的升高,且逐渐成为替代当前需采集肿瘤组织作为标本的无创方法。尽管血循环DNA的来源尚不清楚,通过监测血循环DNA总水平变化及相关肿瘤基因的异常改变,可以实现恶性肿瘤的早期诊断及预后评估。特别是许多国外文献报道,它与淋巴瘤的关系非常密切,无论血循环DNA的定性或定量研究,包括淋巴瘤常见的基因重排或者病毒相关血浆DNA,与淋巴瘤的诊断、治疗反应及预后直接相关。现将近几年国内外血循环DNA在淋巴瘤中的应用进行综述,对研究前景做简单展望。     

Determination of the effectiveness of Pseudorabies marker vaccines in experiments and field trials

The aim of vaccination in an eradication campaign is not only to induce clinical protection, but primarily to stop transmission of infections within and between herds by inducing herd immunity. Consequently, vaccines should be evaluated for their capacity to reduce virus transmission in the population. Glycoprotein E (gE) negative marker vaccines against Pseudorabies virus (PRV) infections in pigs have been evaluated this way in experiments and field studies. PRV infection in groups of (vaccinated) pigs was determined by measuring antibodies against gE of PRV from regularly taken serum samples. For the statistical analysis of the experiments a stochastic susceptible-infectious-removed (SIR) model was used. A measure for the transmission of virus is the reproduction ratio R, which is defined as the average number of secondary cases caused by one typical infectious individual. This implies that an infection will always fade out in a population when R < 1, but the infection can spread massively when R > 1. From several experiments it was shown that R < 1. Field studies showed that the R within herds was still > 1, but by reducing further contacts the R could be reduced to a value below one. This would imply that PRV could be eradicated by means of vaccination. In The Netherlands, an eradication campaign was launched in 1993, and in 2002 the virus was eradicated, as shown by a negligible number of gE-positive pigs. Farmers' organizations have to decide whether or not to stop vaccination.     

Development of cloning vectors and transformation methods for<Emphasis Type="Italic"> Amycolatopsis</Emphasis>

The genus Amycolatopsis is of industrial importance, as its species are known to produce commercial antibiotics. It belongs to the family Pseudonocardiaceae and has an eventful taxonomic history. Initially strains were identified as Streptomyces, then later as Nocardia. However, based on biochemical, morphological and molecular features, the genus Amycolatopsis, containing seventeen species, was created. The development of molecular genetic techniques for this group has been slow. The scarcity of molecular genetic tools including stable plasmids, antibiotic resistance markers, transposons, reporter genes, cloning vectors, and high efficiency transformation protocols has made progress slow, but efforts in the past decade have led to the development of cloning vectors and transformation methods for these organisms. Some of the cloning vectors have broad host range (pRL series) whereas others have limited host range (pMEA300 and pMEA100). The cloning vector pMEA300 has been completely sequenced, while only the minimal replicon (pA-rep) has been sequenced from pRL plasmids. Direct transformation of mycelia and electroporation are the most widely applicable methods for transforming species of Amycolatopsis. Conjugational transfer from Escherichia coli has been reported only in the species A. japonicum, and gene disruption and replacements using homologous recombination are now possible in some strains. Electronic Publication     

大肠杆菌K-12dnaA突变型的R6K整合抑制菌株的多起点染色体复制

大肠杆菌K-12的温度敏感复制发动缺陷突变(dnaA46)菌株LC381不能在42℃中进行染色体复制。在42℃中选取R6K质粒整合抑制菌株,用标记频率测定法测得这一菌株在30℃中染色体复制从正常的复制起点起始,在42℃中则从另外三个起点起始,其中两个曾见报道,把重组突变recA56引入这一菌株,发现由接近正常复制起点起始的染色体复制不受recA突变的影响,由接近正常复制终点起始的染色体复制则受到阻碍,说明由这一位置起始的染色体复制依赖于recA基因。这一实验结果和我们的其他报道相符。     

The chemotaxonomic classification of Korean Campanulaceae based on triterpene,sterol, and polyacetylene contents

The taxonomic usefulness of selected marker compounds was investigated by analyzing the chemotaxonomy of 25 taxa in the Korean Campanulaceae. Our data permit discrimination of the source plants of crude drugs listed in the Korean Pharmacopoeia and the Korean Herbal Pharmacopoeia. Chemotaxonomic analysis methods were validated, and quantitative measurements of six marker compounds were made using HPLC. Marker compound similarities among taxa were identified through multivariate statistical analyses (principal component analysis and hierarchical cluster analysis). The chemical analysis method was validated with regard to linearity, lower limit of detection, lower limit of quantitation, precision, accuracy, and recovery. The analysis revealed differences in the marker compound composition of each genus. Eight genera comprising Adenophora, Codonopsis, Asyneuma, Campanula, Hanabusaya, Platycodon, Wahlenbergia, and Peracarpa clustered according to the chemical classification. The results indicated that the six marker compounds used in this analysis were useful in identifying Korean Campanulaceae. These marker compound data were able to successfully discriminate among the three species that are sold as the crude drug Adenophorae Radix.     

Spiked GBS: a unified,open platform for single marker genotyping and whole-genome profiling

Background

In plant breeding, there are two primary applications for DNA markers in selection: 1) selection of known genes using a single marker assay (marker-assisted selection; MAS); and 2) whole-genome profiling and prediction (genomic selection; GS). Typically, marker platforms have addressed only one of these objectives.

Results

We have developed spiked genotyping-by-sequencing (sGBS), which combines targeted amplicon sequencing with reduced representation genotyping-by-sequencing. To minimize the cost of targeted assays, we utilize a small percent of sequencing capacity available in runs of GBS libraries to “spike” amplified targets of a priori alleles tagged with a different set of unique barcodes. This open platform allows multiple, single-target loci to be assayed while simultaneously generating a whole-genome profile. This dual-genotyping approach allows different sets of samples to be evaluated for single markers or whole genome-profiling. Here, we report the application of sGBS on a winter wheat panel that was screened for converted KASP markers and newly-designed markers targeting known polymorphisms in the leaf rust resistance gene Lr34.

Conclusions

The flexibility and low-cost of sGBS will enable a range of applications across genetics research. Specifically in breeding applications, the sGBS approach will allow breeders to obtain a whole-genome profile of important individuals while simultaneously targeting specific genes for a range of selection strategies across the breeding program.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1404-9) contains supplementary material, which is available to authorized users.     

Genetic diversity in European wheat and spelt breeding material based on RFLP data

Fifty-two winter wheat (Triticum aestivum L.), nine spring wheat, and 20 spelt (Triticum spelta L.) lines representing part of the European breeding germplasm, were assayed for RFLPs (restriction fragment length polymorphisms) with 56 wheat DNA clones and two barley cDNA clones. Objectives of this study were to (1) determine the level of variation for RFLPs in the wheat and spelt breeding lines, (2) characterize the genetic diversity within the European winter wheat germplasm, and (3) evaluate the usefulness of RFLP markers for pedigree analysis and the grouping of wheat and spelt lines of various origins. Seventy-three of the 166 RFLP loci detected with 58 probes and one restriction enzyme were polymorphic for the 81 lines. The percentage of polymorphic loci was greatest for the B genome (58%) and smallest for the D genome (21%). Among the 81 lines, 271 different RFLP bands were detected. RFLP band frequencies of the winter wheat lines differed considerably (0.5) from those of the spring wheat lines at five loci, and from those of the spelt lines at 17 loci. Eight cultivars that had a major impact as progenitors on the development of improved winter wheat cultivars accounted for 93% of the observed RFLP bands in winter wheat. Genetic distance (GD) estimates between two lines ranged between 0.01 and 0.21. Mean GD estimates within winter wheat (0.083), within spring wheat (0.108) and within spelt (0.096) were smaller than between spring and winter wheat (0.114), and greatest between winter wheat and spelt (0.132) and spring wheat and spelt (0.148). Principal coordinate analysis performed on GD estimates revealed a clear separation of wheat and spelt germplasm. Novel spelt lines with various proportions of wheat germplasm were positioned between wheat and traditional spelt lines. The spring wheat lines formed a distinct group at the periphery of the distribution of the winter wheat lines. Subgroupings of the winter wheat lines according to the cluster analysis were in good agreement with their origin, and lines with common ancestors were grouped together.