A proposal for a standard CORBA interface for genome maps

MOTIVATION: The scientific community urgently needs to standardize the exchange of biological data. This is helped by the use of a common protocol and the definition of shared data structures. We have based our standardization work on CORBA, a technology that has become a standard in the past years and allows interoperability between distributed objects. RESULTS: We have defined an IDL specification for genome maps and present it to the scientific community. We have implemented CORBA servers based on this IDL to distribute RHdb and HuGeMap maps. The IDL will co-evolve with the needs of the mapping community. AVAILABILITY: The standard IDL for genome maps is available at http:// corba.ebi.ac.uk/RHdb/EUCORBA/MapIDL.htm l. The IORs to browse maps from Infobiogen and EBI are at http://www.infobiogen.fr/services/Hugemap/IOR and http://corba.ebi.ac.uk/RHdb/EUCORBA/IOR CONTACT: manu@infobiogen.fr, tome@ebi.ac.uk     

Easier threading through web-based comparisons and cross-validations

SUMMARY: We have developed a WWW server for the integration and comparison of protein structure predictions performed by five different servers. Users submit an amino acid sequence to a selected set of these prediction methods. Results are gathered on a web-based page in order to facilitate comparison and analysis. All the alignments are further evaluated through a common threading tool making their comparisons easier. AVAILABILITY: The meta-server is available free at http://www.infobiosud.cnrs.fr/bioserver SUPPLEMENTARY INFORMATION: http://www.infobiosud.cnrs.fr/bioserver/hah1.html     

Evaluation of genetic diversity and population structure of Macqueen’s Bustard Chlamydotis macqueenii in Iran

Capsule: There is low genetic diversity in the Macqueen’s Bustard Chlamydotis macqueenii in Iran.

Aims: To investigate the genetic diversity and population structure of Macqueen’s Bustard in Iran, using two mitochondrial DNA loci.

Methods: Molecular diversity of the mitochondrial cytochrome oxidase c subunit I (COI) gene and part of the mitochondrial control region D-loop (in total 1183 base pairs) were analysed from 26 individual Macqueen’s Bustards from three regions of Iran.

Results: There was little variation in nucleotides and haplotypes in the populations for genes of both CR and COI. The population had free breeding and gene flow between the three study regions in Iran: Petregan, Ferdows and Yazd.

Conclusion: The use of molecular and genetic studies is essential to strengthen the protection of genetic diversity of the Macqueen’s Bustard.     

Online database for mosquito (Diptera,Culicidae) occurrence records in French Guiana

A database providing information on mosquito specimens (Arthropoda: Diptera: Culicidae) collected in French Guiana is presented. Field collections were initiated in 2013 under the auspices of the CEnter for the study of Biodiversity in Amazonia (CEBA: http://www.labexceba.fr/en/). This study is part of an ongoing process aiming to understand the distribution of mosquitoes, including vector species, across French Guiana. Occurrences are recorded after each collecting trip in a database managed by the laboratory Evolution et Diversité Biologique (EDB), Toulouse, France. The dataset is updated monthly and is available online. Voucher specimens and their associated DNA are stored at the laboratory Ecologie des Forêts de Guyane (Ecofog), Kourou, French Guiana. The latest version of the dataset is accessible through EDB’s Integrated Publication Toolkit at http://130.120.204.55:8080/ipt/resource.do?r=mosquitoes_of_french_guiana or through the Global Biodiversity Information Facility data portal at http://www.gbif.org/dataset/5a8aa2ad-261c-4f61-a98e-26dd752fe1c5 It can also be viewed through the Guyanensis platform at http://guyanensis.ups-tlse.fr     

Advances in transgenic animal models and techniques

On May 11th and 12th 2017 was held in Nantes, France, the international meeting “Advances in transgenic animal models and techniques” (http://www.trm.univ-nantes.fr/). This biennial meeting is the fifth one of its kind to be organized by the Transgenic Rats ImmunoPhenomic (TRIP) Nantes facility (http://www.tgr.nantes.inserm.fr/). The meeting was supported by private companies (SONIDEL, Scionics computer innovation, New England Biolabs, MERCK, genOway, Journal Disease Models and Mechanisms) and by public institutions (International Society for Transgenic Technology, University of Nantes, INSERM UMR 1064, SFR François Bonamy, CNRS, Région Pays de la Loire, Biogenouest, TEFOR infrastructure, ITUN, IHU-CESTI and DHU-Oncogeffe and Labex IGO). Around 100 participants, from France but also from different European countries, Japan and USA, attended the meeting.     

Genetic profiling of the critically endangered palm species Medemia argun using newly developed chloroplast DNA markers

Background: Medemia argun is a rare wild palm tree species. Its global existence is assumed to include the main population of about 1000 trees in the Nubian Desert of Sudan and some scattered individuals in southern Egypt. The species had previously been assumed to be extinct, but then reported to be extant about 20 years ago.

Aims: To assess genetic variation and explore population genetic structure of M. argun, through development and analysis of microsatellite markers.

Methods: The genome sequence mining approach was applied in order to identify microsatellites in the chloroplast genome of Bismarckia nobilis, a species closely related of M. argun. A set of 49 markers were designed, and their characteristics are now provided. Seven chloroplast DNA markers were developed for use in the genetic characterisation of this threatened species.

Results: Five markers were found polymorphic in M. argun, which enabled the assessment of the genetic diversity of the species. Significant genetic differentiation was observed among generations and collection sites, accompanied by low genetic variation. The seven markers developed were polymorphic among the wild relatives Hyphaene thebaica and Borassus aethiopum.

Conclusions: This is the first study to report molecular markers for M. argun. Our results suggest that the genetic consequences of population fragmentation in M. argun are beginning to be evident.     

An online database for genome information of agricultural plants

The integration-based genome database provides useful information through a user-friendly web interface that allows analysis of comparative genome for agricultural plants. We have concentrated on the functional bioinformatics of major agricultural resources, such as rice, Chinese cabbage, rice mutant lines, and microorganisms. The major functions are focused on functional genome analysis, including genome projects, gene expression analysis, gene markers with genetic map, analysis tools for comparative genome structure, and genome annotation in agricultural plants.

Availability

The database is available for free at http://nabic.naas.go.kr/     

Micronuclei as a marker for medical screening of subjects continuously occupationally exposed to low doses of ionizing radiation

Context: Genotoxicity assays are widely employed in human biomonitoring studies to assess genetic damage inflicted by genotoxic agents.

Objective: Evaluation of micronuclei (MN) as a screening marker of occupational ionizing radiation (IR) exposure.

Materials and methods: Using micronucleus test, peripheral blood lymphocytes (PBL) of 402 control and exposed subjects were screened for genetic damage.

Results: The mean frequencies of micronucleus test parameters were significantly higher in exposed persons. Increase of micronucleus yield with duration of exposure (DOE) by 0.303MN/year was revealed.

Discussion and conclusion: The obtained data encourage us to consider MN as valuable markers for preventive medical screening of occupationally exposed groups.     

PlantGM: a database for genetic markers in rice (Oryza sativa) and Chinese cabbage (Brassica rapa)

The Plant Genetic Map Database (PlantGM) has been developed as a web-based system which provides information about genetic markers in rice (Oryza sativa) and Chinese cabbage (Brassica rapa). The database has three major parts and functions; (1) Map Search, (2) Marker Search, and (3) QTL Search. At present, the database provides characterization information for about 3258 genetic markers. It has 2800 RFLP and 112 QTL markers related to rice in addition to 321 RFLP and 25 PCR-based markers for Chinese cabbage. In addition, a genetic linkage map was also constructed by using 1,054 markers from 2,912 markers in rice.

Availability

The database is available for free at http://www.niab.go.kr/nabic/PlantGM     

Genotype transposer: automated genotype manipulation for linkage disequilibrium analysis

SUMMARY: The purpose of this work is to provide the modern molecular geneticist with tools to perform more efficient and more accurate analysis of the genotype data they produce. By using Microsoft Excel macros written in Visual Basic, we can translate genotype data into a form readable by the versatile software 'Arlequin', read the Arlequin output, calculate statistics of linkage disequilibrium, and put the results in a format for viewing with the software 'GOLD'. AVAILABILITY: The software is available by FTP at: ftp://xcsg.iarc.fr/cox/Genotype_Transposer/. SUPPLEMENTARY INFORMATION: Detailed instruction and examples are available at: ftp://xcsg.iarc.fr/cox/Genotype&_Transposer/. Arlequin is available at: http://lgb.unige.ch/arlequin/. GOLD is available at: http://www.well.ox.ac.uk/asthma/GOLD/.     

PROSIT,AN ONLINE SERVICE TO CALCULATE PSEUDOROTATIONAL PARAMETERS OF NUCLEOSIDES AND NUCLEOTIDES

The online service PROSIT (Pseudo-Rotational Online Service and Interactive Tool) is a free service available at http://cactus.nci.nih.gov/prosit/ that performs pseudorotational analysis of nucleosides(tides). PROSIT reads the 3D coordinates of nucleosides and returns the pseudorotational phase angle P, puckering amplitude ν_max, and other related information. As examples, the sugar conformations in a parallel-stranded guanine tetraplex and a four-way Holliday junction are presented here.