webFOG: A web tool to map genomic features onto genes

A large number of new genomic features are being discovered using high throughput techniques. The next challenge is to automatically map them to the reference genome for further analysis and functional annotation. We have developed a tool that can be used to map important genomic features to the latest version of the human genome and also to annotate new features. These genomic features could be of many different source types, including miRNAs, microarray primers or probes, Chip-on-Chip data, CpG islands and SNPs to name a few. A standalone version and web interface for the tool can be accessed through: http://populationhealth.qimr.edu.au/cgi-bin/webFOG/index.cgi. The project details and source code is also available at http://www.bioinformatics.org/webfog.     

Construction of a medium-density horse gene map

A medium-density map of the horse genome (Equus caballus) was constructed using genes evenly distributed over the human genome. Three hundred and twenty-three exonic primer pairs were used to screen the INRA and the CHORI-241 equine BAC libraries by polymerase chain reaction and by filter hybridization respectively. Two hundred and thirty-seven BACs containing equine gene orthologues, confirmed by sequencing, were isolated. The BACs were localized to horse chromosomes by fluorescent in situ hybridization (FISH). Overall, 165 genes were assigned to the equine genomic map by radiation hybrid (RH) (using an equine RH(5000) panel) and/or by FISH mapping. A comparison of localizations of 713 genes mapped on the horse genome and on the human genome revealed 59 homologous segments and 131 conserved segments. Two of these homologies (ECA27/HSA8 and ECA12p/HSA11p) had not been previously identified. An enhanced resolution of conserved and rearranged chromosomal segments presented in this study provides clarification of chromosome evolution history.     

Using spectrophotometry and spectral mapping technique for the study of the production of manganese-dependent and manganese-independent peroxidases by Pleurotus ostreatus

The activity of manganese-dependent and manganese-independent peroxidases produced by Pleurotus ostreatus in culture media composed of agro-residues was measured by visible spectrophotometry. The overall enzyme activity and its selectivity were separated by using spectral mapping technique followed by nonlinear mapping. The relationships between the parameters of enzyme production and the composition of culture media and fermentation time was assessed by stepwise regression analysis. Calculations proved that the addition of extract of straw to the culture media significantly decreased the overall production of both enzymes, whereas the selectivity of enzyme production was influenced by amount of potato extract and the concentration of total sugar in the culture media. Enzyme activity depended quadratically on the fermentation time.     

Physical education - new technologies for mapping plant genomes

Locating DNA sequences to specific chromosomal segments is essential for associating genes with phenotypes. It is routinely achieved by segregation analysis using meiotic mapping populations that have also been used to collect phenotypic information. However, meiotic mapping is struggling to cope with the shear volume of sequences emerging from high-throughput (HTP) gene-discovery programs. We describe two approaches, Radiation Hybrid and ‘HAPPY’ mapping, which, in conjunction with meiotic mapping, represent valuable HTP tools in the quest to link genes to phenotypes.     

Mapping multiple QTL using linkage disequilibrium and linkage analysis information and multitrait data

A multi-locus QTL mapping method is presented, which combines linkage and linkage disequilibrium (LD) information and uses multitrait data. The method assumed a putative QTL at the midpoint of each marker bracket. Whether the putative QTL had an effect or not was sampled using Markov chain Monte Carlo (MCMC) methods. The method was tested in dairy cattle data on chromosome 14 where the DGAT1 gene was known to be segregating. The DGAT1 gene was mapped to a region of 0.04 cM, and the effects of the gene were accurately estimated. The fitting of multiple QTL gave a much sharper indication of the QTL position than a single QTL model using multitrait data, probably because the multi-locus QTL mapping reduced the carry over effect of the large DGAT1 gene to adjacent putative QTL positions. This suggests that the method could detect secondary QTL that would, in single point analyses, remain hidden under the broad peak of the dominant QTL. However, no indications for a second QTL affecting dairy traits were found on chromosome 14.     

Genetic Mapping and ENU Mutagenesis

ENU mutagenesis is a potent means to generate novel mutations in the mouse, and the further investigation of these mutations can be logistically demanding. Determination of the map position of a mutation early in its characterization can be extremely useful. We describe how the use of interval haplotype analysis can facilitate this with even small numbers of affected progeny.     

The development of sulfonylurea herbicide-resistant birdsfoot trefoil (Lotus corniculatus) plants from in vitro selection

Summary The use of information from flanking markers to estimate the position and size of the effect of a quantitative trait locus (QTL) lying between two markers is shown to be affected by QTLs lying in neighbouring regions of the chromosome. In some situations the effects of two QTLs lying outside the flanked region are reinforced in such a way that a ghost QTL may be mistakenly identified as a real QTL. These problems are discussed in the framework of a backcross using a regression model as the analytical tool to present the theoretical results. Regression models that use information obtained from three or more nearby markers are shown to be useful in separating the effects of QTLs in neighbouring regions. A simulated data set exemplifies the problem and is analysed by the interval mapping method as well as by the regression model.     

Isolation and characterization of a resistant core peptide of recombinant human granulocyte-macrophage colony-stimulating factor (GM-CSF); confirmation of the GM-CSF amino acid sequence by mass spectrometry.

A trypsin-resistant core peptide of recombinant human granulocyte-macrophage colony-stimulating factor (rhGM-CSF) was isolated and analyzed by high-energy Cs+ liquid secondary-ion (LSI) mass spectrometric analysis. This analysis provided successful detection of the high-mass disulfide-linked core peptide as well as information confirming the existence of disulfide pairing. Similarly, LSI mass spectrometric analysis of the peptide fragments isolated chromatographically from a Staphylococcus aureus V8 protease digest of rhGM-CSF provided rapid confirmation of the cDNA-derived sequence and determination of the existing disulfide bonds between cysteine residues 54-96 and 88-121. Electrospray ionization mass spectrometry was employed to measure the molecular weight of the intact protein and to determine the number of the disulfide bonds in the protein molecule by comparative analysis of the protein before and after reduction with beta-mercaptoethanol.     

Radiation hybrid maps of Medaka chromosomes LG 12, 17, and 22.

The Medaka is an excellent genetic system for studies of vertebrate development and disease and environmental and evolutionary biology studies. To facilitate the mapping of markers or the cloning of affected genes in Medaka mutants identified by forward-genetic screens, we have established a panel of whole-genome radiation hybrids (RHs) and RH maps for three Medaka chromosomes. RH mapping is useful, since markers to be mapped need not be polymorphic and one can establish the order of markers that are difficult to resolve by genetic mapping owing to low genetic recombination rates. RHs were generated by fusing the irradiated donor, OLF-136 Medaka cell line, with the host B78 mouse melanoma cells. Of 290 initial RH clones, we selected 93 on the basis of high retention of fragments of the Medaka genome to establish a panel that allows genotyping in the 96-well format. RH maps for linkage groups 12, 17, and 22 were generated using 159 markers. The average retention for the three chromosomes was 19% and the average break point frequency was approximately 33 kb/cR. We estimate the potential resolution of the RH panel to be approximately 186 kb, which is high enough for integrating RH data with bacterial artificial chromosome clones. Thus, this first RH panel will be a useful tool for mapping mutated genes in Medaka.     

县区生态系统服务分布图编制——以北京市延庆区土壤保持服务为例

地图是直观展示生态系统服务空间分布格局的手段,是确定重要生态保护目标和区域的主要方法。结合制图学理论方法及国家、行业相关制图规范,探讨生态系统服务分布图编制的目标、原则、流程和制图方法。以编制北京市延庆区1 ： 25万土壤保持服务分布图为例,分析了地理基础确定、地理要素取舍以及土壤保持服务分级等关键制图方法,提出了土壤保持服务分布图的编制规范。研究结果表明,编制的图件能够详尽的展示土壤保持服务的分布特征,精细的反映生态系统服务与自然、人文要素的关系。通过详实的图面信息可进一步判别土壤保持服务分布重要区域,这将为区域生态环境保护规划提供重要技术手段。     

Methods for multiple-marker mapping of quantitative trait loci in half-sib populations

In this paper we consider the detection of individual loci controlling quantitative traits of interest (quantitative trait loci or QTLs) in the large half-sib family structure found in some species. Two simple approaches using multiple markers are proposed, one using least squares and the other maximum likelihood. These methods are intended to provide a relatively fast screening of the entire genome to pinpoint regions of interest for further investigation. They are compared with a more traditional single-marker least-squares approach. The use of multiple markers is shown to increase power and has the advantage of providing an estimate for the location of the QTL. The maximum-likelihood and the least-squares approaches using multiple markers give similar power and estimates for the QTL location, although the likelihood approach also provides estimates of the QTL effect and sire heterozygote frequency. A number of assumptions have been made in order to make the likelihood calculations feasible, however, and computationally it is still more demanding than the least-squares approach. The least-squares approach using multiple markers provides a fast method that can easily be extended to include additional effects.     

An expanded comparative map of bovine chromosome 27 targeting dairy form QTL regions

At present, the density of genes on the bovine maps is extremely limited and current resolution of the human-bovine comparative map is insufficient for selection of candidate genes controlling many economic traits of interest in dairy cattle. This study describes the chromosomal mapping of 10 selected gene-associated markers to bovine linkage and radiation hybrid maps to improve the breakpoint resolution in the human-bovine comparative map near two previously identified quantitative trait loci for the linear type trait, dairy form. Two regions of conserved synteny not previously described are reported between the telomeric region of bovine chromosome 27 (BTA27) and human chromosome 3 (HSA3) p24 region and between the HSA4q34.1 region and BTA8. These data increase the number of genes positioned on the bovine gene maps, refine the human-bovine comparative map, and should improve the efficiency of candidate gene selection for the dairy form trait in cattle.     

Detection and validation of EST-SSR markers associated with sugar-related traits in sugarcane using linkage and association mapping

Sugar-related traits are of great importance in sugarcane breeding. In the present study, quantitative trait loci (QTL) mapping validated with association mapping was used to identify expressed sequence tag-simple sequence repeats (EST-SSRs) associated with sugar-related traits. For linkage mapping, 524 EST-SSRs, 241 Amplified Fragment Length Polymorphisms, and 10 genomic SSR markers were mapped using 283 F₁ progenies derived from an interspecific cross. Six regions were identified using Multiple QTL Mapping, and 14 unlinked markers using single marker analysis. Association analysis was performed on a set of 200 accessions, based on the mixed linear model. Validation of the EST-SSR markers using association mapping within the target QTL genomic regions identified two EST-SSR markers showing a putative relationship with uridine diphosphate (UDP) glycosyltransferase, and beta-amylase, which are associated with pol and sugar yield. These functional markers can be used for marker-assisted selection of sugarcane.     

DOMAIN: a flexible modelling procedure for mapping potential distributions of plants and animals

This paper briefly reviews some limitations associated with the application of existing modelling procedures to conservation ecology, and describes a new procedure (DOMAIN) which avoids these problems. The procedure computes potential distributions based on a range-standardized, point-to-point similarity metric and provides a simple, robust method for modelling potential distributions of plant and animal species. DOMAIN offers advantages over similar methods in its ability to operate effectively using only presence records and a limited number of biophysical attributes. The use of a continuous similarity function gives DOMAIN increased flexibility as an heuristic tool, suitable for application in survey design, reserve selection and potential mapping of rare and common species. Potential distributions were computed for two Australian marsupial bettong species (Aepyprymnus rufescens Gray and Bettongia tropica Wakefield) using DOMAIN and two alternative models. Of the three procedures, the DOMAIN model produced distribution patterns that were most consistent with the known ecology of the species, and most appropriate for survey design.     

Assignment of 117 genes from HSA5 to the porcine IMpRH map and generation of a dense human-pig comparative map

Twenty-two and eight significant quantitative trait loci for economically important traits have been located on porcine chromosomes (SSC) 2q and SSC16 respectively, both of which have been shown to correspond to human chromosome 5 (HSA5) by chromosome painting. To provide a comprehensive comparative map for efficient selection of candidate genes, we assigned 117 genes from HSA5 using a porcine radiation hybrid (IMpRH) panel. Sixty-six genes were assigned to SSC2 and 48 to SSC16. One gene was suggested to link to SSC2 markers and another to SSC6. One gene did not link to any gene, expressed sequence tag or marker in the map, including those in the present investigation. This study demonstrated the following: (1) SSC2q21-q28 corresponds to the region ranging from 74.0 to 148.2 Mb on HSA5q13-q32 and the region from 176.0 to 179.3 Mb on HSA5q35; (2) SSC16 corresponds to the region from 1.4 to 68.7 Mb on HSA5p-q13 and to the region from 150.4 to 169.1 Mb on HSA5q32-q35 and (3) the conserved synteny between HSA5 and SSC2q21-q28 is interrupted by at least two sites and the synteny between HSA5 and SSC16 is also interrupted by at least two sites.     

Cytogenetic and molecular mapping of the wheat-Aegilops longissima chromatin breakpoints in powdery mildew-resistant introgression lines

The amount of alien chromatin introgressed in eight wheat/Ae. longissima Pm13 recombinant lines, involving breakpoints on the short arms of wheat chromosomes 3B and 3D, was evaluated by cytogenetic and molecular approaches. For each line the residual homologous synaptic ability of the recombinant chromosome in its proximal wheat and distal alien portion was estimated through meiotic analyses. Subsequently, telocentric and RFLP mapping were used to assess the genetic distance from the wheat centromere to the wheat/Ae. longissima breakpoints. One 3B recombinant line was distinguished from the other four by the chromosome pairing and telocentric mapping analyses. RFLP analysis succeeded in differentiating the remaining four lines into two groups. Chromosome pairing and telocentric mapping of the three 3D recombinant lines suggested that all had distinct breakpoints. However, the RFLP data could not discriminate between the two more proximal translocations. Physical locations for some RFLP loci were determined by a comparison of genotypes and C-banding karyotypes. This showed a considerable expansion of the genetic map compared to its physical length.     

Assignment of 115 genes from HSA9 and HSA14 to SSC1q by RH mapping to generate a dense human-pig comparative map

A large number of significant QTL for economically important traits including average daily gain have been located on SSC1q, which, as shown by chromosome painting, corresponds to four human chromosomes (HSA9, 14, 15 and 18). To provide a comprehensive comparative map for efficient selection of candidate genes, 81 and 34 genes localized on HSA9 and HSA14 respectively were mapped to SSC1q using a porcine 7000-rad radiation hybrid panel (IMpRH). This study, together with the cytogenetic map (http://www2.toulouse.inra.fr/lgc/pig/cyto/genmar/htm/1GM.HTM), demonstrates that SSC1q2.1-q2.13 corresponds to the region ranging from 44.6 to 63.2 Mb on HSA14q21.1-q23.1, the region from 86.5 to 86.8 Mb on HSA15q24-q25, the region from 0.9 to 27.2 Mb on HSA9p24.3-p21, the region from 35.1 to 38.0 Mb on HSA9p13, the region from 70.3 to 79.3 Mb on HSA9q13-q21 and the region from 96.4 to 140.0 Mb on HSA9q22.3-q34. The conserved synteny between HSA9 and SSC1q is interrupted by at least six sites, and the synteny between HSA14 and SSC1q is interrupted by at least one site.     

Molecular characterization of the porcine MHC class I region

A porcine cosmid library was screened with a human MHC class I cDNA. Four positive clones were isolated and mapped with different restriction endonucleases. Altogether nine SLA class I genes were identified and their positions located within restriction maps. Sizes of class I homologous DNA sequences varied between 3600 and 5800bp. The distances between these regions ranged from 11900 to 22200bp.     

Principles of electroanatomic mapping

Electrophysiologic testing and radiofrequency ablation have evolved as curative measures for a variety of rhythm disturbances. As experience in this field has grown, ablation is progressively being used to address more complex rhythm disturbances. Paralleling this trend are technological advancements to facilitate these efforts, including electroanatomic mapping (EAM). At present, several different EAM systems utilizing various technologies are available to facilitate mapping and ablation. Use of these systems has been shown to reduce fluoroscopic exposure and radiation dose, with less significant effects on procedural duration and success rates. Among the data provided by EAM are chamber reconstruction, tagging of important anatomic landmarks and ablation lesions, display of diagnostic and mapping catheters without using fluoroscopy, activation mapping, and voltage (or scar) mapping. Several EAM systems have specialized features, such as enhanced ability to map non-sustained or hemodynamically unstable arrhythmias, ability to display diagnostic as well as mapping catheter positions, and wide compatibility with a variety of catheters. Each EAM system has its strengths and weaknesses, and the system chosen must depend upon what data is required for procedural success (activation mapping, substrate mapping, cardiac geometry), the anticipated arrhythmia, the compatibility of the system with adjunctive tools (i.e. diagnostic and ablation catheters), and the operator's familiarity with the selected system. While EAM can offer significant assistance during an EP procedure, their incorrect or inappropriate application can substantially hamper mapping efforts and procedural success, and should not replace careful interpretation of data and strict adherence to electrophysiologic principles.