Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains

Background

Genetic markers and maps are instrumental in quantitative trait locus (QTL) mapping in segregating populations. The resolution of QTL localization depends on the number of informative recombinations in the population and how well they are tagged by markers. Larger populations and denser marker maps are better for detecting and locating QTLs. Marker maps that are initially too sparse can be saturated or derived de novo from high-throughput omics data, (e.g. gene expression, protein or metabolite abundance). If these molecular phenotypes are affected by genetic variation due to a major QTL they will show a clear multimodal distribution. Using this information, phenotypes can be converted into genetic markers.

Results

The Pheno2Geno tool uses mixture modeling to select phenotypes and transform them into genetic markers suitable for construction and/or saturation of a genetic map. Pheno2Geno excludes candidate genetic markers that show evidence for multiple possibly epistatically interacting QTL and/or interaction with the environment, in order to provide a set of robust markers for follow-up QTL mapping.We demonstrate the use of Pheno2Geno on gene expression data of 370,000 probes in 148 A. thaliana recombinant inbred lines. Pheno2Geno is able to saturate the existing genetic map, decreasing the average distance between markers from 7.1 cM to 0.89 cM, close to the theoretical limit of 0.68 cM (with 148 individuals we expect a recombination every 100/148=0.68 cM); this pinpointed almost all of the informative recombinations in the population.

Conclusion

The Pheno2Geno package makes use of genome-wide molecular profiling and provides a tool for high-throughput de novo map construction and saturation of existing genetic maps. Processing of the showcase dataset takes less than 30 minutes on an average desktop PC. Pheno2Geno improves QTL mapping results at no additional laboratory cost and with minimum computational effort. Its results are formatted for direct use in R/qtl, the leading R package for QTL studies. Pheno2Geno is freely available on CRAN under “GNU GPL v3”. The Pheno2Geno package as well as the tutorial can also be found at: http://pheno2geno.nl.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0475-6) contains supplementary material, which is available to authorized users.     

Use of generic fast gradient liquid chromatography–tandem mass spectroscopy in quantitative bioanalysis

Short narrow analytical HPLC columns have been used successfully with high linear flow-rates and combined with mass spectrometric detection to produce a generic approach to quantitative bioanalysis. The approach has been used to validate several assays in the low ng/ml region and an example is given in this paper. When combined with a simple solid-phase extraction process the need for complicated, time consuming method development has been removed for the majority of pharmaceutical compounds. The approach takes advantage of not only the extra selectivity of the MS–MS detector but the excellent resolution and peak shape produced by gradient elution.     

庚型肝炎病毒NS5区蛋白鼠单克隆抗体的制备

庚型病毒性肝炎是近年来世界上才确认的一种新型肝炎［１～３］。庚型肝炎病毒（ＨＧＶ）呈世界性分布,经血液传播为主,也可母婴传播。ＨＧＶ容易形成持续性感染,类似ＨＩＶ和ＨＣＶ。据粗略估计,我国大约有１００万～１０００万ＨＧＶ携带者。因此,ＨＧＶ已成为继乙...     

Enzyme-linked immunosorbent assays for the measurement of blood group A and B glycosyltransferase activities

ELISA assays have been developed for (1–3)N-acetylgalactosaminyltransferase (blood group A transferase) and (1–3)galactosyltransferase (blood group B transferase) activities. In these assays, microtitre plates coated with the bovine serum albumin conjugate of a synthetic Fuc1–2Gal-R acceptor substrate are incubated with the appropriate nucleotide donor (UDP-GalNAc or UDP-Gal) and human serum as the enzyme source. The resulting trisaccharide products Fuc1–2(GalNAc1–3)Gal-R-BSA or Fuc1–2(Gal1–3)Gal-R-BSA are detected and quantified with monoclonal antibodies selected not to cross-react with the substrate structure. With less than a microliter of human serum, product formation is proportional to enzyme concentration and to time of incubation of up to 90 min.     

Settlement of the diazotrophic,phytoeffective bacterial strain Pantoea agglomerans on and within winter wheat: An investigation using ELISA and transmission electron microscopy

The aim of this study was to investigate the ability of Pantoea agglomerans, a plant growth-promoting bacterium, to colonize various regions and tissues of the wheat plant (Triticum aestivum L.) by using different inoculation methods and inoculum concentrations. In addition, the enzyme-linked immunosorbent assay (ELISA) and transmission electron microscopy (TEM) were used to determine: (a) the ability of the bacterial cells to grow and survive both on the surface and within internal tissue of the plant and (b) the response of the plant to bacterial infection. After inoculation, cells of the diazotrophic bacterial strain P. agglomerans were found to be located in roots, stems and leaves. Colony development of bacterial cells was only detected within intercellular spaces of the root and on the root surface. However, single bacterial cells were observed in leaves and stems on the surface of the epidermis, in the vicinity to stomatal cells, within intercellular spaces of the mesophyll and within xylem vessels. Inoculated bacterial cells were found to be able to enter host tissues, to multiply in the plant and to maintain a delicate relationship between endophyte and host. The density of bacterial settlement in the plant in all experiments was about 10⁶ to 10⁷ cells per mL root or shoot sap. Establishment was confirmed by a low coefficient of variation of ELISA means at these concentrations.     

Gene fusion vectors based on the gene for staphylococcal protein A

Two plasmid vectors, containing the gene coding for staphylococcal protein A and adapted for gene fusion, have been constructed. These vectors will allow fusion of any gene to the protein A gene, thus giving hybrid proteins which can be purified, in a one-step procedure, by IgG affinity chromatography. As an example of the practical use of such vectors, the protein A gene has been fused to the lacZ gene of Escherichia coli. E. coli strains containing such plasmids produce hybrid proteins with both IgG binding and β-galactosidase activities. The hybrid protein(s) can be immobilized on IgG-Sepharose by its protein A moiety with high efficiency without losing its enzymatic activity and they can be eluted from the column by competitive elution with pure protein A. The fused protein(s) also binds to IgG-coated microtiter wells which means that the in vivo product can be used as an enzyme conjugate in ELISA tests.     

以人工合成多肽为抗原的戊型肝炎病毒抗体检测方法的建立和评价

酶联法是ＨＥＶ感染的主要检测方法,多采用基因表达产物为抗原。近来由于人工合成多肽抗原克服了基因重组抗原制备复杂、非特异结构多、难以纯化的缺点,已广泛用于多种病毒感染的检测。根据已发表的ＨＥＶ氨基酸序列的保守性及亲水性等特点,设计合成了两个多肽ＥＳＰ１和ＥＳＰ２,分别位于ＯＲＦ２和ＯＲＦ３区,以此为混合抗原建立了检测ＨＥＶ抗体的间接ＥＬＬＳＡ法,与市售优质试剂比较,其阳性符合率为９７．７５％,阴性符合率为９９．４３％,总符合率为９８．８６％。该方法灵敏度高、特异性强、安全快速,是检测ＨＥＶ感染和流行病学调查的理想方法。     

Dendroclimatic potential of dendroanatomy in temperature-sensitive Pinus sylvestris

The most frequently and successfully used tree-ring parameters for the study of temperature variations are ring width and maximum latewood density (MXD). MXD is preferred over ring width due to a more prominent association with temperature. In this study we explore the dendroclimate potential of dendroanatomy based on the first truly well replicated dataset. Twenty-nine mature living Pinus sylvestris trees were sampled in North-eastern Finland at the cool and moist boreal forest zone, close to the latitudinal tree line, where ring width, X-ray MXD as well as the blue intensity counterpart MXBI were compared with dendroanatomical parameters. Maximum radial cell wall thickness as well as anatomical MXD and latewood density appeared to be the most promising parameters for temperature reconstruction. In fact, these parameters compare favorably to MXD derived from X-ray techniques as well as MXBI, in terms of shared variation and temperature correlations across frequencies and over time. The reasons for these results are thought to be the unprecedentedly high measurement resolution of the anatomical technique, which provide the optimal resolution – the cell – whereas X-ray techniques have a slightly lower resolution and BI techniques even lower. While the results of this study are encouraging, further tests on longer and multigenerational chronologies are required to more generally and fully assess the dendroclimate potential of anatomical parameters.     

HLA class II alleles and measles virus-specific cytokine immune response following two doses of measles vaccine

Measles virus-specific T cells and the production of cytokines play a critical role in the immune response following measles immunization. To understand the genetic factors that influence variation in IFN- and IL-4 responses following measles immunization and to provide insight into the factors influencing both cellular and humoral immunity to measles, we assessed associations between human leukocyte antigen (HLA) class II genes and measles-specific Th1 and Th2-type cytokine responses in peripheral blood lymphocytes from 339 children previously vaccinated with two doses of measles-mumps-rubella vaccine (MMR-II). Median values for measles-specific IFN- and IL-4 secretion levels were 40.73 and 9.71 pg/ml, respectively. The global tests suggested associations between measles-specific IFN- response and alleles of the DRB1 and DQB1 loci (P=0.07 and P=0.02, respectively). Specifically, DRB1*0301, *0901, and *1501 alleles were significantly associated with IFN- secretion. The alleles that suggested evidence of an HLA association with IL-4 secretion were DRB1*0103, *0701, and *1101. Th1 cytokine responses and DQB1 allele associations revealed that the alleles with the strongest association with IFN- secretion were DQB1*0201, *0303, *0402, and *0602. Specific alleles with a suggestive association with low measles-specific Th2 cytokine responses were DQB1*0202 and *0503. In addition, DPB1*0101, *0201, and *0601 alleles provided suggestive evidence of an HLA association with measles-induced IFN- response, while DPB1*0501 was associated with an IL-4 response. These data suggest that IFN- and IL-4 cytokine responses to measles may be genetically restricted in part by HLA class II genes, which in turn can restrict the cellular immune response to measles vaccine.     

猴T淋巴细胞趋向性病毒1型双抗原夹心ELISA检测试剂盒的研制

目的研制灵敏度和特异性高的检测实验猴血清中T淋巴细胞趋向性病毒-1型（STLV-1型）／E体的双抗原夹心ELISA（dsELISA）检测试剂盒。方法采用经原核表达系统表达并纯化的人T淋巴细胞白血病病毒-1型（HTLV-1型）的Env蛋白作为包被用抗原,建立了检测STLV-1的dsELISA诊断方法。通过优化反应条件和筛选试剂,确定了dsELISA诊断试剂盒的相关条件,并经敏感性、特异性和重复性试验考查该试剂盒质量。结果试剂盒特异性好,批内重复试验变异系数（CV）〈7％,批间重复试验CV〈10％。对200份猴血清进行随机检测,与国际公认的诊断试剂盒（美国BioReliance公司）的符合率为97％。结论本试剂盒可初步应用于临床上实验猴STLV-1型抗体的检测。