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Microbial Symbiosis at UW-Madison

http://www.microbes.wisc.edu/symbiosis/index.html

The microbial symbiosis community at UW-Madison has positioned itself on the cutting edge of symbiosis research. Over twenty laboratories, including four faculty hired as part of the Symbiosis Cluster, are exploring beneficial microbial symbiosis in plants, animals, and biofilms. This interdisciplinary group brings together numerous faculty and students from departments and schools across the university. Symbiosis activities include monthly seminars, journal club, and a manuscript review; as well as a yearly symbiosis-related conference. Please join us as we delve into the spectacular diversity of interactions between microbes and the world! If you are interested in receiving the UW-Madison Weekly Symbiosis Newsletter, please email This e-mail address is being protected from spam bots, you need JavaScript enabled to view it .

Lab Activity - 5th-8th grade - "The Secret Lives of Nematodes"

http://www.accessexcellence.org/AE/ATG/data/released/0653-SamanthaOrchard/

Nematodes are small roundworms found in the soil. Different nematode species have different lifestyles, with some causing disease in insects, plants, or even humans. This activity focuses on insect-parasitic (entomopathogenic) nematodes. Students will collect soil samples, bait the soil with a living insect larva and monitor what happens in the coming weeks. Some of the insects will die, which presents a "murder mystery" for the students to solve. Typically, insects will die from a variety of causes (e.g. infection by nematodes or fungus or possibly other "natural" causes like hunger/dehydration) and students may only be able to solve the mystery for those insects killed by nematodes. The nematodes, having killed and consumed the insect from inside and reproduced, will leave the insect at some point to search for a new insect to kill and eat. It is at this point that the progeny nematodes can be harvested and visualized with a dissecting microscope. The students can then test their hypothesis that the nematodes killed the insect (if that is their hypothesis!) by using the collected nematodes to try to kill a new insect. This activity requires about 4 class periods (about half an hour each) each spread 1-2 weeks apart.
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Stock Lab, The University of Arizona

http://ag.arizona.edu/ento/faculty/stock/index.htm

Research in the Stock Lab spans the fields of Nematology, Entomology, and Plant Pathology encompassing classical and molecular-based systematics, ecology, biodiversity, and evolution, and the development of biological control strategies using nematodes to control economically important pests.

Plant Nematode Genomics Group, NC State University

http://www.pngg.org

The Plant Nematode Genomics Group (PNGG) integrates knowledge and research of free-living and parasitic nematodes and exploits opportunities in post-genomic biology to make strides in understanding the basic mechanisms of parasitism.

Meloidogyne hapla genome resources (open source):
• M. hapla BLAST (10X)
• M. hapla Mega BLAST (10X)
• M. hapla GBROWSE resource
• M. hapla Assembly download (contigs fasta, 51.3 MB file size)

N. tobacum data (open source):
• Assemblies of the N. tabacum data are available for download. Files have been broken up to make downloads more manageable in terms of size as well as to allow you to download only subsets of the files of interest to individual researchers.

Society of Nematologists

http://www.nematologists.org/

The Society of Nematologists is an international organization formed to advance the science of nematology in both its fundamental and economic aspects. To serve this purpose, the Society of Nematologists acts as an agency for the exchange of information, holds regular meetings, and promotes and extends knowledge in all phases of nematology. The Society operates on a nonprofit basis exclusively for the accomplishment of these educational and scientific goals.

The Journal of Nematology at PubMed Central

http://www.ncbi.nlm.nih.gov/pmc/journals/506/

Volume 1, No.1 January 1969 thru Volume 40, No.3 September 2008.

The Nematology Journal Collection including The Journal of Nematology, Nematologia Mediterranea, and Nematropica can be found at:
http://palmm.fcla.edu/nematode/

Nematode.net genome sequencing center

http://www.nematode.net/index.php

Nematode.net is a resource for investigating gene sequences from nematode genomes. The database is an outgrowth of the parasitic nematode EST project at Washington University's Genome Sequencing Center (GSC), St Louis. Nematode.net currently provides sequence data and analyses (NemaGene EST cluster consensus and BLAST search tools), functional classifications (gene ontology, NemaPath KEGG associations, intestinal transcriptome, and nematode protein families) and information concerning the ongoing generation of nematode genome data. Nematode phylogeny is also presented. Links to publications associated with the project are provided. Made available on the Web by the Washington University in St. Louis.

Nematode diagnostics

http://nematode.unl.edu/wormdiag.htm

This page provides access to a laboratory manual to assist in the molecular identification of nematodes. Chapters cover various techniques including nematode smash/DNA isolation. There is also an illustrated key for the diagnosis of plant parasitic and freshwater nematodes and an index to all the nematode species mentioned on the main website. This resource forms part of the Plant and Insect Parasitic Nematode site hosted by the University of Nebraska-Lincoln.

Plant Nematology Lab, University of Leeds

http://www.biology.leeds.ac.uk/nem/

Home page of the Plant Nematology Lab within the Centre for Plant Sciences (CPS), part of the Faculty of Biological Sciences at the University of Leeds. General information is given on the lab and its facilities and scientific approach, along with background information on the nematode problem, the crops studied, biosafety, and developing world applications. Staff contact details and a list of publications and links are provided, and there is a facility to search the site. The site also makes available a short PowerPoint presentation entitled 'Feed the World Food for Thought: Can GM crops help feed the world?' by H.J. Atkinson, Association for Science Education, sponsored by BBRSC. Made available on the Web by the Plant Biotechnology Information Unit, University of Leeds.

WormBook : the online review of C. elegans biology

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=wormbook.TOC

WormBook is a comprehensive online publication of containing over 100 peer-reviewed chapters on aspects of the biology of C. elegans and related nematodes. Topics covered include: genetics and genomics, molecular biology, cell biology, post-embryonic development, sex determination, the germ line, developmental control mechanisms, signal transduction, neurobiology and behaviour, nematode evolution and ecology and wormMethods. The book was published in 2005 by WormBook and is made available here by the National Center for Biotechnology Information (NCBI) from their 'Bookshelf' where a collection of biomedical books have been adapted for the Web.

Common names of plant diseases

http://www.apsnet.org/online/common/

This site gives access to a searchable database of plant pathogens and the common names of the diseases that they cause. Content is derived from, and expands on, a 1994 print publication of the same name by the American Phytopathological Society (APS). Diseases are listed by plant species and include those caused by bacteria, nematodes, fungi, viruses, viroids and other graft-transmissible pathogens. The common names in these listings are the official names for use in APS journals and other publications.

KinBase

http://www.kinase.com/kinbase/

KinBase is database containing information on all protein kinase genes found in the human, mouse, sea urchin, fruit fly (Drosophila melanogaster), nematode worm (Caenorhabditis elegans), yeast (Saccharomyces cerevisiae), Dictyostelium, Tetrahymena and Monosiga brevicollis genomes. The database is searchable by gene name, domain, or by kinase classification at the group, family or subfamily level. KinBase can also be queried by sequence similarity, using a Blast server.

Model organisms guide

http://www.ncbi.nlm.nih.gov/About/model/

The Model Organisms Guide produced by the US National Center for Biotechnology (NCBI) gives information on commonly used model organisms, and acts as a gateway to genomic resources such as sequence information and mapping both within and beyond the NCBI. The guide covers mammalian models (mouse and rat), the flowering plant Arabidopsis thaliana), and other non-mammalian models as follows: Archaea; microbes; Drosophila melanogaster (the fruit fly); malarial parasites, the nematode Caenorhabditis elegans; retroviruses; Saccharomyces cerevisiae (brewer's yeast); Danio rerio; (the zebrafish) and the social amoeba Dictyostelium discoideum. Made available on the Web by the US National Center for Biotechnology Information.

TranspoGene

http://transpogene.tau.ac.il/

The TranspoGene database covers transposed elements (TEs) located inside protein-coding genes of seven species: human, mouse, chicken, zebrafish, fruit fly, nematode and sea squirt. TranspoGene contains information regarding the specific type and family of TEs, genomic and mRNA location, sequence, supporting transcript accession and alignment to the TE consensus sequence. The database also contains host gene specific data: gene name, genomic location, Swiss-Prot and RefSeq accessions, diseases associated with the gene and splicing pattern. The entire database can be downloaded as flat files. Made available on the Web by the Gil Ast laboratory in the Department of Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Israel.

WWW virtual library : model organisms

http://ceolas.org/VL/mo/

The WWW Virtual Library for model organisms is a page of key links to resources specific to biological model organisms found on the Web. The main model organisms covered are E. coli (bacterium), S. cerevisiae (yeast), Dictyostelium (slime mould), Drosophila (fruit fly), and Xenopus (African clawed frog). Other model organisms listed include C. elegans (nematode worm), Arabidopsis (mustard plant), zebrafish, and mouse. This site is regularly updated and is provided on the Web by Dr Gerard Manning.

USDA-ARS Nematology Laboratory

http://www.ars.usda.gov/main/site_main.htm?modecode=12-75-29-00

The Nematology Laboratory is based at the Beltsville Agricultural Research Center (BARC) and comes under the auspices of the US Department of Agriculture's (USDA) Agricultural Research Service (ARS). The Laboratory works to develop environmentally safe control strategies for plant-parasitic nematodes and methods for utilizing nematodes as control agents of insect pests, thereby promoting agricultural sustainability, assuring food safety, improving water quality, and providing linkage to integrated pest management systems. Information is provided about the lab, its research projects, details of publications including nematode basics, nematode common names, plant parasitic nematodes, history of the lab, staff research interests and publications, news and events and details of career opportunities.

AppaDB, Max-Planck Institute

http://pristionchus.org/

AppaDB, a Pristionchus pacificus database, integrates the genomic data of P. pacificus, comprising the physical map, genetic linkage map, EST and BAC end sequence and hybridization data. This developing database serves as a repository to search and find any information regarding physical contigs or genetic markers required for mapping of mutants. Additionally, it provides a platform for the Caenorhabditis elegans community to compare nematode genetic data in an evolutionary perspective. Made available on the web by the Max-Planck Institute for Developmental Biology.

NEMBASE "4"

http://www.nematodes.org/nembase4/

NEMBASE is an online database providing access to the sequence and associated meta-data currently being generated as part of the Edinburgh-Wellcome Trust Sanger Institute parasitic nematode EST project. Users may query the database on the basis of BLAST annotation, sequence similarity, expression profiles, nematode lifecycle stage-specific expression, and by cDNA library-specific expression levels. NEMBASE also features an interactive Java-based tool (SimiTri) which allows the simultaneous display and analysis of the relative similarity relationships of groups of sequences to three different databases.

Wolbachia-like endosymbiont of Onchocerca volvulus

http://www.sanger.ac.uk/Projects/Wolbachia/

The Wolbachia-like endosymbiont of Onchocerca volvulus genome page is provided by The Wellcome Trust Sanger Institute, as part of a microbial sequencing effort focusing on pathogens and model organisms. Onchocerca volvulus is a nematode that causes onchocerciasis (river blindness) in West Africa and Central America. An overview of the project is provided and unfinished assembled shotgun sequences are available for searching on a BLAST server and may be downloaded via FTP. Presently, there are 6 contigs from 6 clones. The Artemis DNA viewer/annotator software (free to download) may be used to analyse and annotate sequences of interest to the researcher. This project is funded by Beowulf Genomics.

Istituto di Nematologia Agraria Applicata ai Vegetali (INAAV)

http://www.inaav.ba.cnr.it/inaav2en.htm

This site outlines the INAAV's major areas of research: the identification, systematics and taxonomy of plant-parasitic nematodes; life history and host-parasite interactions; and control of pest nematode species. The projects are arranged under general headings of: biodiversity; biological control strategies; chemical, physical and agronomic control strategies; host-parasite relationship; host and parasite genetics and relationships between nematodes and other organisms. A link is provided to the Institute's journal, Nematologia Mediterranea.

Brugia malayi sequencing and mapping project

http://www.sanger.ac.uk/Projects/B_malayi/

The Brugia malayi Sequencing and Mapping Project page is provided by The Wellcome Trust Sanger Institute, as part of a sequencing effort in collaboration with Mark Blaxter's lab at the University of Edinburgh to compare the genomes of related nematode species. Information is provided on the background to the project, progress, and data release. A Blast server is available for searching the sequence data, and the data is available for download via FTP. The site also provides links to the Pathogen Genomics project and other Wellcome Trust Sanger Institute sequencing projects. This project is funded by The Wellcome Trust Sanger Institute.

H. contortus sequencing

http://www.sanger.ac.uk/Projects/H_contortus/

The parasitic nematode Haemonchus contortus sequencing page is provided by The Wellcome Trust Sanger Institute, as part of the Pathogen Genomics sequencing effort which aims to sequence the genomes of organisms relevant to human and animal health. In addition to an overview of the project, a database containing the latest data is available by FTP from the site and can be searched using the Blast server provided. The Artemis DNA sequence viewer and annotater software (free to download) may be used to analyse and annotate sequences of interest to the researcher. Links are provided to the Pathogen Genomics project and other Welcome Trust Sanger Institute sequencing projects. This project is funded by the Wellcome Trust.

C. elegans movies

http://www.bio.unc.edu/faculty/goldstein/lab/movies.html

This page offers a selection of internal and external time lapse movies of the nematode C.elegans, illustrating techniques and different developmental stages including embryos and larvae. All movies require QuickTime. Each movie page provides links to external sites and related PubMed articles, where appropriate. These movies are provided as part of the Goldstein Laboratory pages at the University of North Carolina at Chapel Hill, US.

Bacteria - animal symbiosis site

http://web.uconn.edu/mcbstaff/graf/Sym.html

Home page of a research group in the Department of Molecular and Cell Biology at the University of Connecticut which investigates how bacteria colonize the digestive tract of animals without causing disease. This site describes the groups work on four bacteria - animal symbionts namely the nematode (Steinernema carpocapsae), aphids (Aphidoidea), Hawaiian squid (Euprymna scolopes) and (Hirudo medicinalis), the medicinal leech. The site also provides a general introduction to symbiosis and details of postgraduate research opportunities in the group. This resource has been created by Joerg Graf from the Department and Elaine S. Mirkin, a freelance writer.

Organization of Nematologists of Tropical America

http://www.ontaweb.org/

The website of the Organization of Nematologists of Tropical America (ONTA) provides information on publications, officers and upcoming meetings. The Organisation was founded in 1967 by a group of nematologists from the subtropics and tropics to share information on the management of plant-parasitic nematodes. Since then it has expanded to include free-living and insect-parasitic species. Via an external link you can access full-text articles of the Organisation's peer reviewed, biannual journal Nematropica, from 1990 onwards (PDF). The site also contains a general introduction to nematodes, a browsable directory of members and links to other nematode sites. This site is offered in English and Spanish.

International Symbiosis Society

http://iss-symbiosis.org/

The goals of the International Symbiosis Society are to:

• disseminate information to the public, students, educators and researchers about symbiotic interactions:
• advance scientific research:
• provide members with access to the journal Symbiosis:
• and,  serve as a forum where researchers can interact.

 Symbiosis, the journal, link.

The Bordenstein Laboratory

http://bordensteinlab.vanderbilt.edu/

The Bordenstein Laboratory has broad interests in microbial-host interactions that have relevance to basic biology and applied biomedicine at multiple biological levels (i.e., genetic, ecological, evolutionary, and genomic), including the:

• Molecular evolution and applications of mobile elements in bacteria
• Role of bacterial symbionts in eukaryotic speciation
• Genetics of animal-microbe interactions
• Symbiotic control of human diseases