MedicCyc: a biochemical pathway database for Medicago truncatula

MOTIVATION: There is an imperative need to integrate functional genomics data to obtain a more comprehensive systems-biology view of the results. We believe that this is best achieved through the visualization of data within the biological context of metabolic pathways. Accordingly, metabolic pathway reconstruction was used to predict the metabolic composition for Medicago truncatula and these pathways were engineered to enable the correlated visualization of integrated functional genomics data. Results: Metabolic pathway reconstruction was used to generate a pathway database for M. truncatula (MedicCyc), which currently features more than 250 pathways with related genes, enzymes and metabolites. MedicCyc was assembled from more than 225,000 M. truncatula ESTs (MtGI Release 8.0) and available genomic sequences using the Pathway Tools software and the MetaCyc database. The predicted pathways in MedicCyc were verified through comparison with other plant databases such as AraCyc and RiceCyc. The comparison with other plant databases provided crucial information concerning enzymes still missing from the ongoing, but currently incomplete M. truncatula genome sequencing project. MedicCyc was further manually curated to remove non-plant pathways, and Medicago-specific pathways including isoflavonoid, lignin and triterpene saponin biosynthesis were modified or added based upon available literature and in-house expertise. Additional metabolites identified in metabolic profiling experiments were also used for pathway predictions. Once the metabolic reconstruction was completed, MedicCyc was engineered to visualize M. truncatula functional genomics datasets within the biological context of metabolic pathways. Availability: freely accessible at http://www.noble.org/MedicCyc/     

The Medicago Genome Initiative: a model legume database

The Medicago Genome Initiative (MGI) is a database of EST sequences of the model legume MEDICAGO: truncatula. The database is available to the public and has resulted from a collaborative research effort between the Samuel Roberts Noble Foundation and the National Center for Genome Resources to investigate the genome of M.truncatula. MGI is part of the greater integrated MEDICAGO: functional genomics program at the Noble Foundation (http://www.noble.org ), which is taking a global approach in studying the genetic and biochemical events associated with the growth, development and environmental interactions of this model legume. Our approach will include: large-scale EST sequencing, gene expression profiling, the generation of M.truncatula activation-tagged and promoter trap insertion mutants, high-throughput metabolic profiling, and proteome studies. These multidisciplinary information pools will be interfaced with one another to provide scientists with an integrated, holistic set of tools to address fundamental questions pertaining to legume biology. The public interface to the MGI database can be accessed at http://www.ncgr.org/research/mgi.     

A flexible forward simulator for populations subject to selection and demography

This article introduces a new forward population genetic simulation program that can efficiently generate samples from populations with complex demographic histories under various models of natural selection. The program (SFS_CODE) is highly flexible, allowing the user to simulate realistic genomic regions with several loci evolving according to a variety of mutation models (from simple to context-dependent), and allows for insertions and deletions. Each locus can be annotated as either coding or non-coding, sex-linked or autosomal, selected or neutral, and have an arbitrary linkage structure (from completely linked to independent). AVAILABILITY: The source code (written in the C programming language) is available at http://sfscode.sourceforge.net, and a web server (http://cbsuapps.tc.cornell.edu/sfscode.aspx) allows the user to perform simulations using the high-performance computing cluster hosted by the Cornell University Computational Biology Service Unit.     

Effects of density on lek-site selection by Black Grouse Tetrao tetrix in the Alps

Capsule: The Black Grouse is a primarily lekking species, but low population density and lack of suitable habitat can lead to the establishment of non-lekking populations.

Aims: To understand if differences in density could be related to differences in the lekking system, if there were differences in lek-site selection, and if there was a direct effect of habitat on the lek size.

Methods: We compared lek sizes between two Black Grouse populations with different male population densities as estimated by distance sampling. We considered land-cover categories, landscape metrics and orographic variables and computed the Ivlev’s Electivity Index to evaluate habitat selection of males in the two study areas. A general linear model was used to assess the relationship between lek size and habitat variables.

Results: We could not demonstrate the direct effect of density on the displaying behaviour but we found strongly different patterns of lek-site selection and different effects of habitat on lek size according to the population density.

Conclusions: We concluded that habitat normally considered as high quality and habitat complexity may play different roles in selection by solitary versus lekking males when different population densities are considered.     

Brazilian genetic database of chromosome X

The X chromosome is a singular source of information in population genetics, anthropological research and in forensic cases. Thus, many researchers have been interested in characterizing X chromosome markers in different populations. The Brazilian Genetic Database of Chromosome X (BGBX—Banco Genético Brasileiro do Cromossomo X) website is freely available in Portuguese and English versions and was developed with the main purpose of compiling all Brazilian population genetic data for X chromosome short tandem repeats (X-STRs) markers published in scientific journals searchable via PubMed. Furthermore, this database presents other relevant information concerning X-STRs, such as genetic and physical locations, allele structure, nomenclature, mutation rates, primers described in the literature and likelihood ratio calculation. The entire scientific community is now encouraged to submit their X-STR population genetic data to this website, available at http://www.bgbx.com.br. Regarding future prospects of BGBX, the authors intend to expand the website with data and information of X-linked insertion–deletion polymorphisms.     

Transformer‐4 version 2.0.1, a free multi‐platform software to quickly reformat genotype matrices of any marker type,and archive them in the Demiurge information system

Transformer‐4 version 2.0.1 (T4) is a multi‐platform freeware programmed in java that can transform a genotype matrix in Excel or XML format into the input formats of one or several of the most commonly used population genetic software, for any possible combination of the populations that the matrix contains. T4 also allows the users to (i) draw allozyme gel interpretations for any number of diploid individuals, and then generate a genotype matrix ready to be used by T4; and (ii) produce basic reports about the data in the matrices. Furthermore, T4 is the only way to optionally submit ‘genetic diversity digests’ for publication in the Demiurge online information system ( http://www.demiurge-project.org ). Each such digest undergoes peer‐review, and it consists of a geo‐referenced data matrix in the tfm4 format plus any ancillary document or hyperlink that the digest authors see fit to include. The complementarity between T4 and Demiurge facilitates a free, safe, permanent, and standardized data archival and analysis system for researchers, and may also be a convenient resource for scientific journals, public administrations, or higher educators. T4 and its converters are freely available (at, respectively, http://www.demiurge-project.org/download_t4 and http://www.demiurge-project.org/converterstore ) upon registration in the Demiurge information system ( http://demiurge-project.org/register ). Users have to click on the link provided on an account validation email, and accept Demiurge's terms of use (see http://www.demiurge-project.org/termsofuse ). A thorough user's guide is available within T4. A 3‐min promotional video about T4 and Demiurge can be seen at http://vimeo.com/29828406 .     

FABSIM: a software for generating FST distributions with various ascertainment biases

We have developed a software that applies ascertainment bias on simulated DNA sequences and calculates F(ST) on them, so they can be used to generate neutral distributions that are appropriate to test whether the genetic differentiation of a particular gene between populations is compatible with neutral evolution, or, on the contrary, suggests local adaptation by natural selection. AVAILABILITY: FABSIM is available from http://www.snpator.com/public/downloads/aRamirez/FABSIM/.     

Selection of source material for introduction of the locally rare and threatened fern species Asplenium septentrionale

Background: Forked spleenwort, Asplenium septentrionale, is a mainly petrophilous fern species in European mountains and rare on acidic siliceous rocks in lowland areas of the continent, where habitats are fragmented and populations isolated. In Estonia, the single extant population is very small, occupies a restricted area and is threatened by human disturbances. An introduction project of the species was prepared to form new populations in new protected sites using ex-situ propagated young sporophytes as transplantation material.

Aims: To obtain data on the species recruitment population biology and provide context information for selecting donor plant material.

Methods: We sampled three regional/local donor populations. First, we carried out a laboratory breeding experiment to evaluate the populations’ ability for intra-gametophytic selfing. Second, to estimate differences in fitness of offspring among the populations, we grew young sporophyte plants in a pot experiment under controlled conditions in a common garden.

Results: The Estonian population showed very high capacity (90%) for intra-gametophytic selfing, as well as high rate of sporophytic mortality (83%), but the rates are comparable to one of the reference populations in Finland. However, plants of Estonian population were smaller.

Conclusions: The Estonian population may represent a unique pre-adapted or locally adapted genotype; therefore, it needs more efficient protection in its present location. Planting material for introduction should be collected from the local population, as the best locally adapted. Only in the risk of severe environmental change and of extinction, several neighbouring populations could be pooled to maximise genetic diversity.     

Proteome reference maps of Medicago truncatula embryogenic cell cultures generated from single protoplasts

Using a combination of two-dimensional gel electrophoresis (2-DE) protein mapping and mass spectrometry (MS) analysis, we have established proteome reference maps of Medicago truncatula embryogenic tissue culture cells. The cultures were generated from single protoplasts, which provided a relatively homogeneous cell population. We used these to analyze protein expression at the globular stages of somatic embryogenesis, which is the earliest morphogenetic embryonic stage. Over 3000 proteins could reproducibly be resolved over a pI range of 4-11. Three hundred and twelve protein spots were extracted from colloidal Coomassie Blue-stained 2-DE gels and analyzed by matrix-assisted laser desorption/ionization-time of flight MS analysis and tandem MS sequencing. This enabled the identification of 169 protein spots representing 128 unique gene products using a publicly available expressed sequence tag database and the MASCOT search engine. These reference maps will be valuable for the investigation of the molecular events which occur during somatic embryogenesis in M. truncatula. The proteome reference maps and supplementary materials will be available and updated for public access at http://semele.anu.edu.au/.     

quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation

quantiNemo is an individual-based, genetically explicit stochastic simulation program. It was developed to investigate the effects of selection, mutation, recombination and drift on quantitative traits with varying architectures in structured populations connected by migration and located in a heterogeneous habitat. quantiNemo is highly flexible at various levels: population, selection, trait(s) architecture, genetic map for QTL and/or markers, environment, demography, mating system, etc. quantiNemo is coded in C++ using an object-oriented approach and runs on any computer platform. Availability: Executables for several platforms, user's manual, and source code are freely available under the GNU General Public License at http://www2.unil.ch/popgen/softwares/quantinemo.     

Sample size calculations for surveys to substantiate freedom of populations from infectious agents

We develop a Bayesian approach to sample size computations for surveys designed to provide evidence of freedom from a disease or from an infectious agent. A population is considered "disease-free" when the prevalence or probability of disease is less than some threshold value. Prior distributions are specified for diagnostic test sensitivity and specificity and we test the null hypothesis that the prevalence is below the threshold. Sample size computations are developed using hypergeometric sampling for finite populations and binomial sampling for infinite populations. A normal approximation is also developed. Our procedures are compared with the frequentist methods of Cameron and Baldock (1998a, Preventive Veterinary Medicine34, 1-17.) using an example of foot-and-mouth disease. User-friendly programs for sample size calculation and analysis of survey data are available at http://www.epi.ucdavis.edu/diagnostictests/.     

PDB2MultiGIF: A Web Tool to Create Animated Images of Molecules

A new web tool, PDB2MultiGIF (http://www.dkfz-heidelberg.de/spec/pdb2mgif/),which converts the topological information (atom types, 3D coordinates, molecular connectivity) of molecules (given in PDB format [1]) to a series of animated images (in GIF Format) [2] is described. The molecular visualisation program RASMOL [3] is used to generate the images.Electronic Supplementary Material available.     

Developing a quantitative index as a pragmatic aid to assessing implementation of European Union Birds Directive site protection measures for individual species

Capsule: A multi-element index is developed to help support decisions with respect to the establishment and review of national networks of European Union (EU) Special Protection Areas (SPAs).

Aims: To develop an index based on biological criteria which can be used to assess the sufficiency of protected area network coverage for national populations of individual bird species.

Methods: A Site Provision Index (SPI) was derived from data on species’ national and international distribution, population size, habitat use and site-fidelity. It was tested against the results of past UK policy and independent expert judgement.

Results: Index values were calculated for all regularly occurring UK birds for which the EU Birds Directive indicates that SPA provision should be considered. Index values and expert opinion on the percentage of populations of species expected to be found in a national network of protected areas were highly correlated. Indices also strongly correlated with existing provision of SPA protection for populations. Residuals from this regression relationship highlight objectively those species where consideration of further SPA provision may be necessary.

Conclusion: The SPI can provide a decision-support tool, through a form of gap analysis, to help identify where there is a significant difference between current protected area provision for a species and the level of provision that might be expected relative to other species with similar distribution and ecology.     

Tradescantia Bioassays as Monitoring Systems for Environmental Mutagenesis: A Review

Since the early studies on the genetic effects of chemical and physical agents, species and clones of Tradescantia have been used as experimental subjects, by virtue of a series of favorable genetic characteristics. Bearing just six pairs (2n = 12) of large, easily observable chromosomes, cells from almost every part of the plant, from the root tips to the developing pollen tube, yield excellent material for cytogenetic studies.

As a consequence of the intensive use of Tradescantia in genetic studies, a series of genetic characteristics have been found that offer opportunities for the detection of agents affecting the stability of the genome. At least five such characteristics have been selected as endpoints for the establishment of assays to evaluate mutagenesis. Three of these, root-tip mitosis, pollen-tube, and microspore mitosis are essentially chromosome aberration assays, wherein one observes and evaluates the visible damage in the chromosomes. A fourth, the stamen-hair mutation assay (Trad-SHM), is a point mutation mitotic assay based on the expression of a recessive gene for flower color in heterozygous plants. The fifth assay is a cytogenetic test based on the formation of micronuclei (Trad-MCN) that result from chromosome breakage in the meiotic pollen mother cells.

This article examines the characteristics and fundamentals of the Trad-MCN and the Trad-SHM assays and reviews the results obtained to date with these systems in the assessment of environmental mutagenesis.     

Kleptoparasitism in gulls Laridae at an urban and a coastal foraging environment: an assessment of ecological predictors

Capsule: Kleptoparasitism in gulls occurred at a greater rate at an urban compared with a coastal site. Population density and prey size predicted the rate of kleptoparasitism at the urban site.

Aims: To investigate and assess the ecological variables associated with kleptoparasitism among gulls at urban and rural sites.

Methods: Field observations were conducted at Brancaster (coastal rural) and Billingsgate Market (urban) to examine differences in the rate of kleptoparasitism in mixed-species flocks of gulls. Four key variables (prey size, population density, season and species) were assessed as predictors of kleptoparasitism.

Results: Generalized linear models revealed significant effects on kleptoparasitism rate of site, population density and prey size, and two-way interactions between these main terms. Population density and prey size differed significantly between sites, but population density appeared to predict the rate of kleptoparasitism.

Conclusion: Kleptoparasitism may well aid invasion and increase the range of environments a gull can tolerate by helping them meet their energy needs in novel environments where normal foraging behaviours are difficult to implement.     

Sexual dimorphism and sex determination in Black-necked Grebes Podiceps nigricollis: on the need to account for geographical variation in morphology and sex ratio

Capsule: The sex of Black-necked Grebes Podiceps nigricollis in Spain can be determined successfully using a locally derived discriminant function analysis (DFA) but a function derived from a North American population was not successful.

Aims: To determine the extent of sexual size dimorphism in the Black-necked Grebe and develop discriminant functions based on morphometric data. We also assessed the accuracy of visual sexing by fieldworkers with different levels of experience and compared the discriminant function for European birds with one for North American birds, in order to determine the geographical specificity of the function.

Methods: We used a data set of 370 Black-necked Grebes from a European population throughout the non-breeding seasons of 2008–11 in the Odiel saltmarshes (Spain), as well as published data from North America, to compare the accuracy of DFAs developed for European and North American populations when applied to the same population.

Results: Males were significantly larger than females for all body measurements. The DFA with the highest success rate included one single linear dimension (head-bill length), showing an efficiency of 88.5% in the same sample used to build the function and up to 91.5% in independent samples of birds. The more experienced ringer showed higher accuracy in visual sexing than the less experienced one (84 vs. 70%), although self-consistency in sex assignment of a given individual was similar. The function developed for European birds performed poorly for American birds (79.1% sexed correctly) and vice versa (18.4% sexed correctly).

Conclusion: Morphological and sex ratio differences between European and American subspecies both contribute to the discrepancy in the success rate. This illustrates the need for caution when applying discriminant functions developed in one bird population to individuals elsewhere.     

AncestryPainter: A Graphic Program for Displaying Ancestry Composition of Populations and Individuals

Ancestry composition of populations and individuals has been extensively investigated in recent years due to advances in the genotyping and sequencing technologies. As the number of populations and individuals used for ancestry inference increases remarkably, say more than 100 populations or 1000 individuals, it is usually challenging to present the ancestry composition in a traditional way using a rectangular graph. To address this issue, we developed a program, AncestryPainter, which can illustrate the ancestry composition of populations and individuals with a rounded and nice-looking graph to save space. Individuals are depicted as length-fixed bars partitioned into colored segments representing different ancestries, and the population of interest can be highlighted as a pie chart in the center of the circle plot. In addition, AncestryPainter can also be applied to display personal ancestry in a way similar to that for displaying population ancestry. AncestryPainter is publicly available at http://www.picb.ac.cn/PGG/resource.php.     

Mutational analysis of a catalytically important loop containing active site and substrate-binding site in Escherichia coli phytase AppA

A phytase from Escherichia coli, AppA, has been the target of protein engineering to reduce the amount of undigested phosphates from livestock manure by making phosphorous from phytic acid available as a nutrient. To understand the contribution of each amino acid in the active site loop to the AppA activity, alanine and glycine scanning mutagenesis was undertaken. The results of phytase activity assay demonstrated loss of activity by mutations at charged residues within the conserved motif, supporting their importance in catalytic activity. In contrast, both conserved, non-polar residues and non-conserved residues tended to be tolerant to Ala and/or Gly mutations. Correlation analyses of chemical/structural characteristics of each mutation site against mutant activity revealed that the loop residues located closer to the substrate have greater contribution to the activity of AppA. These results may be useful in efficiently engineering AppA to improve its catalytic activity.

Abbreviations: AppA: pH 2.5 acid phosphatase; CSU: contacts of structural units; HAPs: histidine acid phosphatases; SASA: solvent accessible surface area; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SSM: site-saturation mutagenesis; WT: wild type