This article is in press in 'Protist' (Vol. 150(2)) and it is posted with permission from Urban and Fischer Publishers.
The World Wide Web is a true revolution in communication. In regard to the study of protists, the web has a plethora of informational web sites. In this Protist News, I would like to briefly describe an assortment of interesting and useful sites. My list is illustrative and critical rather than all-inclusive, so please forgive me if I fail to include your favorite site or even your own site.
Unfortunately this article as journal text is not yet on-line and therefore cannot utilize the full power and depth of hyperlinks, but I will list the URL's and you must then type them into your browser to link to them. If you get tired typing and prefer using a browser to be able to click directly to the various sites, this article will also be available on-line (http://www.lifesci.ucla.edu/hhmi/simpson/news.html) at the Protist web site (http://www.uni-koeln.de/math-nat-fak/botanik/protist/index.html) and also linked to my lab home page at http://www.lifesci.ucla.edu/hhmi/simpson/.
There are references in the ancient Chinese and Greek writings to malaria, but of course the etiology was not known. The study of protists began with the discovery of the microscope and its utilization by Robert Hooke and Antony van Leeuwenhoek. There are excellent sites on both Hooke (http://www.ucmp.berkeley.edu/history/hooke.html) and Leeuwenhoek (http://www.ucmp.berkeley.edu/history/leeuwenhoek.html). Leeuwenhoek was a true pioneer and is credited for making the first observations of bacteria, protozoa and cells from metazoans. He used single lens microscopes with extremely short focal lengths. Functional reconstructions of his microscopes are described at http://www.sirius.com/~alshinn/ and detailed plans for construction of a working replica are also provided (http://www.sirius.com/~alshinn/Leeuwenhoekplans.html). Leeuwenhoek's studies had essentially no impact on science at that time. This was not due to a lack of communication since he wrote many letters to the Royal Society in London for almost 30 years and he entertained many important visitors to his home with glimpses of his "animalcules". A modern reexamination of several long lost specimens sent to the Royal Society by Leeuwenhoek is described at http://www.sciences.demon.co.uk/wavintr.htm. The main reason is probably the absence of a proper conceptual framework into which his observations would fit, perhaps caused partially but not entirely by his proclivity towards keeping his single lens microscope methods a trade secret. The total lack of any meaningful influence of Leeuwenhoek on science in the 1700's meant that the true functional discovery of protists awaited the development of compound light microscopes corrected for both spherical and chromatic aberrations, that anyone could build or purchase. This fascinating history is documented in the interesting web site on the "History of the Light Microsope" (http://www.utmem.edu/personal/thjones/hist/hist_mic.htm). The true paradigm shift - the articulation of the theory by Schleiden and Schwann that all organisms are composed of cells - finally occurred in 1839, soon after development of the achromatic lens in 1827.
The realization that many diseases are caused by unicellular microorganisms was another major conceptual change that greatly stimulated research on protists. In fact, further advances in the study of protists were closely tied with the development of tropical medicine. Some major advances in knowledge were the discovery of the Leishmania flagellates as the causal agents of kala-azar by Leishman and Donovan in 1900-1903, the discovery of the trypanosome as the causal agent of animal and human sleeping sickness by Bruce in 1903, the discoveries of the malaria parasite in blood and the malaria parasite in the mosquito vector by Laveran in 1880 and Ross in 1897, and the discovery that the T. cruzi trypanosome present in reduviid insects was the causal agent of a chronic human disease by Chagas in 1910. These are described and literature references are provided in a web site I created for a course in molecular parasitology (http://www.lifesci.ucla.edu/hhmi/C168/lslecture1.html).
Images of protists are available in several web sites. A site at http://megasun.bch.umontreal.ca/protists/gallery.html shows a variety of protists selected by their inclusion in the mitochondrial genome sequencing project. Information about the taxonomy, culture and classification is also presented. Another web site with a more comprehensive collection of images and information of protists is http://ant.c.dna.affrc.go.jp/WWW/PDB/Images/menuE.html. The images are also organized in a functional sense at http://ant.c.dna.affrc.go.jp/WWW/PDB/Images/menu2E.html#subject. An excellent site with more than 5000 images of protists is at the "Protist Information Server at http://mtlab.biol.tsukuba.ac.jp/WWW/ .
Another web site with protist information and images is at http://www.kent.wednet.edu/staff/kloschky/Protists%20Folder/protists.html. The comprehensive web site on the Euglenoid protists by Triemer at http://lifesci.rutgers.edu/~triemer/index.htm is also an excellent resource of images and information.
Other web sites which include images and life cycles of protist parasites are http://www.biosci.ohio-state.edu/~parasite/taxonomic.html, http://www-micro.msb.le.ac.uk/224/Parasitol.html, http://www.life.sci.qut.edu.au/LIFESCI/darben/paramast.htm, and http://www.cdfound.to.it/HTML/atlas.htm).
The medically important protozoal parasites, Entamoeba (http://www.lshtm.ac.uk/mp/bcu/enta/homef.htm), Giardia (http://vm.cfsan.fda.gov/~mow/chap22.html), Cryptosporidium (http://www.cellsalive.com/parasit.htm, http://www.cdc.gov/ncidod/diseases/crypto/sources.htm, http://vm.cfsan.fda.gov/~mow/chap24.html), Trypanosoma cruzi (http://www.who.int/ctd/html/chag.html, http://www.sentex.net/~iamat/sp.html), and Leishmania ( http://www.who.int/ctd/html/leis.html ) have their own web sites. And of course there are several valuable web sites on the Plasmodium protists and malaria (http://www.malaria.org/, http://www.malaria.org/BGINFO.HTM , http://www.med.monash.edu.au/micro/malaria/who.html ) . This is where the study of protists merges with the study of the diseases caused by these organisms. Obviously, due to a variety of reasons such as biomedical funding and interest in ameliorating the human diseases, there are more researchers currently working on the protozoal parasites than on free-living protists. Nevertheless, important basic contributions to knowledge have been made using parasitic protists as model systems.
A list of the major protist culture collections can be found at http://megasun.bch.umontreal.ca/protists/pcco.html. This includes the major ATCC collection at: http://www.atcc.org/ .
An interesting phylogenetic systematics site which has information on protists is http://www.ucmp.berkeley.edu/alllife/eukaryotasy.html. The Maddisons' "Tree of Life" is a "phylogenetic navigator" of over 1380 World Wide Web pages containing systematic and phylogenetic information about the diversity of life. For example, a Tree of Life site on the "basal eukaryotes" is located at http://www.ucmp.berkeley.edu/protista/basalprotists.html .
A site for the International Society for Evolutionary Protistology can be found at http://megasun.bch.umontreal.ca/isep/isep.html .
The NCBI Taxonomy Homepage, which is operationally very important for those of us that enter protist sequences into Genbank or wish to recover them, can be found at http://www3.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html . In case you would like to complain to someone about the taxonomic status of your favorite organism (as I did when Genbank insisted on putting my Leishmania tarentolae sequences under "Sauroleishmania!), you can find the list of expert advisors for the NCBI taxonomy at http://www.ncbi.nlm.nih.gov/Taxonomy/Taxresources/taxcontributors.html#theprotists . The specific guidelines and conventions for the NCBI taxonomy can be found at http://www.ncbi.nlm.nih.gov/Taxonomy/Taxresources/guidelines.html .
An attempt to provide a current and comprehensive list of email addresses for many researchers in the field of protistology can be found at : http://www.uga.edu/protozoa/names.htm.
There are a variety of courses which have to varying extent put some or all of the course material on-line. Most of the courses I am familiar with deal with the parasitic protists. A course on Parasitology by Fred Opperdoes which includes much information on the protists is at: http://www.icp.ucl.ac.be/~opperd/parasites/ . An informative site with material on "Protozoa as Human Parasites" is at http://www-micro.msb.le.ac.uk/224/Parasitol.html . A site by Titus Bradley with specific information on "Malaria and Drug resistance" is at http://www-micro.msb.le.ac.uk/224/Bradley/Bradley.html . A course by myself, David Campbell and Pat Johnson on Molecular Parasitology which mainly dealt with the parasitic protists can be found at: http://www.lifesci.ucla.edu/hhmi/C168/ .
Probably the most useful type of Protist web sites are those covering the various genome sequencing projects. This includes the sequence databases and organism-specific blast servers.
The African trypanosome Genome Project site at Cambridge University is at: http://parsun1.path.cam.ac.uk/. This links to the T. brucei EST web site at http://parsun1.path.cam.ac.uk/est.htm and the T. brucei chromosome nomenclature site at http://parsun1.path.cam.ac.uk/xsome.htm . The related T. brucei Genome Project site at TIGR is at http://www.tigr.org/tdb/mdb/tbdb/index.html. The TIGR site has a useful Blast server at http://www.tigr.org/tdb/mdb/tbdb/seq_search.html where one can search sequences against the current BAC, P1 and Sheared DNA Sequence Database. Another parasite-specific Blast server can be found at: http://www.ebi.ac.uk/parasites/parasite_blast_server.html .
The UK Leishmania Genome Network web site at http://www.ebi.ac.uk/parasites/leish.html has links to a site with Leishmania chromosome maps at http://www.ebi.ac.uk/parasites/LGN/chromsum.html , Leishmania EST sequences at http://www.ebi.ac.uk/parasites/LGN/leishest.html , and an extremely useful Leishmania Genome Directory at http://www.ebi.ac.uk/parasites/LGN/GenDir/coverpage.html which has genes organized in a functional manner. The Leishmania Genome Group in Seattle has a useful site at http://204.203.14.2/lmjf/ and the NCBI site for the Leishmania chromosome 1 is at http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/paltik?gi=13580&db=Genome .
Genome mapping information for Plasmodium falciparum is available at http://www.wehi.edu.au/MalDB-www/genomeInfo/MapData/MapData.html, and a genomic sequence tag database for this organism is available athttp://parasite.arf.ufl.edu/path/pfgstp/index.html . The NCBI malaria genome site at http://www.ncbi.nlm.nih.gov/Malaria/ is a useful link to both the sequences obtained at NCBI and at the Sanger laboratory. The direct site for chromosomes 1, 3, 4, 9 and 13 from the Sanger lab is at http://www.sanger.ac.uk/Projects/P_falciparum/. A recent link to the complete Plasmodium chromosome 3 sequence is at: http://www.sanger.ac.uk/Projects/P_falciparum/mal3/ . A P. falciparum home page from the Sanger lab is at http://www.sanger.ac.uk/Projects/P_falciparum/ . The TIGR P. falciparum Genome Database site for chromosomes 2, 10, 11 and 14 is at http://www.tigr.org/tdb/edb/pfdb/pfdb.html . The Stanford P. falciparum database site for chromosome 12 is at http://sequence-www.stanford.edu/group/malaria/index.html .
A genome web site for Toxoplasma is available at http://www.ebi.ac.uk/parasites/toxo/toxpage.html. The Toxoplasma EST Project site is at http://genome.wustl.edu/est/toxo_esthmpg.html, and clustered EST sequences can be found at http://www.cbil.upenn.edu/ParaDBs/Toxoplasma/index.html.
A site for EST sequences from Cryptosporidium parvum is found at http://medsfgh.ucsf.edu/id/CpTags/home.html.
A useful web site that has updated codon bias tables for many protist parasites is at http://www.ebi.ac.uk/parasites/cutg.html.
Sequence database of organelles also exist. MitBase at http://www.ebi.ac.uk/htbin/Mitbase/mitbase.pl is a "Comprehensive and Integrated Mitochondrial DNA Database" which is almost completed. It will include the mitochondrial genomes of several protists in addition to higher eukaryotes. GoBase at http://megasun.bch.umontreal.ca/gobase/gobase.html is a relational sequence database of mitochondrial genomes. It is stated to be a "taxonomically broad organelle genome database that organizes and integrates diverse data related to organelles". It will in the future include chloroplast sequences and sequences of prokaryotes thought to be related to the bacterial ancestors of mitochondria and chloroplasts.
And finally, my own U-insertion/deletion edited sequence database at http://www.lifesci.ucla.edu/RNA/trypanosome/database.html contains sequences in GCG format of pre-edited and unedited maxicircle genes from trypanosomatid protists. The data is provided both in the form of clickable maps of the maxicircle genomes and a Table of all the genes organized by species and gene. A useful "map" format is used to show the alignment of the pre-edited genomic sequences with the mature edited RNA sequences and the corresponding amino acid translations of the edited sequences. This preserves the U-deletion information which is lost otherwise. U-insertion information is preserved as lower case u's. Alignments of the overlapping guide RNAs and edited mRNAs are also provided at http://www.lifesci.ucla.edu/RNA/trypanosome/grnas.html . In addition, several published multiple ribosomal RNA alignments of kinetoplastids used to construct phylogenetic trees are also provided at http://www.lifesci.ucla.edu/RNA/trypanosome/alignments.html . A guide RNA database is also available at: http://www.biochem.mpg.de/~goeringe/gRNA/gRNAseqs.html, and a kinetoplast minicircle sequence database (with a somewhat distorted picture of Douglas Barker!) is available at http://www.ebi.ac.uk/parasites/kDNA/Source.html . And last but not least, my U-insertion/deletion web site at http://www.lifesci.ucla.edu/RNA/trypanosome/index.html contains selected recent results, a list of literature references, upcoming scientific meetings, a Bulletin Board for comments and discussion, and names and emails of researchers in this field.
The World Wide Web is a marvelously chaotic landscape of valuable and also not so valuable information. One inherent problem with web sites is a gradual decline in usefulness due to benign neglect; it is easy to create a site but difficult to continuously update it. Also, servers fail and URL's change. Another perhaps more serious problem is the authentication of information provided on any specific site. There is no peer review process and one must rely on the creator of the site for supplying the correct information. Nevertheless, it is clear from this cursory glance at the enormous amount of information available on the subject of protists that the web has become extremely valuable and even essential as a resource for the working scientist.
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