Protist Web Alert
From Parasites to Life in Space!
The World Wide Web is a true international revolution in
communication for science as well as for society in general. The amount
of information available is truly astounding, with the main problems
being the lack of organization, the absence of ready authentication, and
the entropic tendency towards benign neglect of updating the
information. This section will provide a necessarily opinionated review
of new and interesting web sites related to the study of protists.
Please send me (simpson@hhmi.ucla.edu) any
interesting web sites for review, together with your own critical
evaluation if you want to limit the editorial bias!
Molecular Parasitology Network web site (http://www.rna.ucla.edu/par/molpar/):
This under construction web site is a portal to the Molecular
Parasitology Network, which was created by L.S. at the Woods Hole
Molecular Parasitology Meeting in September, 2000, as a "virtual"
international scientific society to further this field of research,
which covers not only parasitic protists but also parasitic worms. It
has working links to the following sites: (1) Members of Molecular
Parasitology Network. (2) Parasite Genome Projects. (3) Parasite
sequence databases. (4) Vectors available. (5) Laboratory Protocols. (6)
Postdoctoral and faculty positions available. (7) Postdoctoral and
faculty positions wanted. (8) Scientific Meetings. (9) A Bulletin Board.
(10) Virtual courses. (11) Funding Agencies. (12) Fellowships and
Prizes. The "Members" site at http://www.arc.ucla.edu/mpn/faculty.cfm
should be very useful and the engine used could serve as a model for
other virtual scientific associations in that it offers the participant
the ability to log on and upgrade their own information. My students
find the "Parasite Genome" site at http://www.rna.ucla.edu/par/ a useful
portal to most of the parasite genome project web sites, specific
databases and blast servers. The "Bulletin Board" site at http://www.rna.ucla.edu/par/molpar/bull.html
provides a threaded bulletin board for ongoing and archived discussions
about any subject in this field (but is yet unfortunately
underutilized!). The "Positions Available" site at http://www.rna.ucla.edu/par/molpar/positions%20avail.htm
is already proving useful for researchers seeking postdocs and postdocs
seeking positions. The "Vectors" site provides links to several
locations providing vector sequences and maps. In regard to this, I
would like to make a plea for labs that provide online vector sequences
to present them as text files in standard Genbank format together with
features, since most current analysis programs such as Vector NTI can
import these and map the features automatically. Otherwise one must
manually enter feature positions into the raw sequences.
All in all, a fabulous site, if I must say so myself!
Uridine-insertion/deletion RNA Editing web site (http://www.rna.ucla.edu/trypanosome/index.html):
This site contains information on this unusual type of RNA
modification that occurs in the mitochondrion of kinetoplastid protists.
It contains a list of researchers in the field, a Bulletin Board,
definitions of the jargon, announcements of meetings, and a selective
list of recent interesting results in the field (suffers from benign
neglect, unfortunately). It also points towards the major specialized
databases in this field: (1) The minicircle DNA database (with a
somewhat distorted photo of Douglas Barker!) (http://www.ebi.ac.uk/parasites/kDNA/Source.html).
This mainly provides pointers to the available Genbank minicircle
sequences for different species. (2) The Edited Sequence Database (http://www.rna.ucla.edu/trypanosome/database.html).
This database contains sequences of mitochondrial genes and cryptogenes
from kinetoplastid protozoa. Edited mRNA sequences and translated amino
acid sequences are also provided. The sequences are in GCG format and
can be obtained as HTML files either by clicking the gene in the genomic
maps, or by clicking the gene name in the Table. A novel "map" format
provides the edited RNA sequence aligned with the genomic DNA sequence
and the translated amino acid sequence; both U-deletions and
U-insertions are indicated by gaps in the edited sequence or the genomic
sequence. In the Leishmania tarentolae genomic map, the sequences
of the maxicircle-encoded gRNAs are also indicated. For Trypanoplasma
borreli, the sequences of the known gRNA genes encoded in the 180 kB
component I DNA are provided. Several published alignments of nuclear
rRNAs of kinetoplastids are also provided in the proper formats for
running standard phylogenetic programs (I encourage everyone who has
such alignments to send them to me for posting, since they are not
otherwise available in any databases).
I am prevented by modesty to put a value judgment on this valuable
site.
DictyBase – An Online Informatic Resource for Dictyostelium
(http://dictybase.org/):
The purpose of this site is to provide a centralized source for
information about Dictyostelium discoideum and related organisms
and to facilitate communication between researchers. The linked sites
include: (1) What's New. (2) Learn About Dictyostelium ( a nice
educational section that features many beautiful mpg and avi movies. I
would however recommend that some instruction be provided to the novice
web surfer as to how to run these movie formats on their browser and
their platform. (3) Search. (4) Dicty Annual Conference (Great places
and nice informal photos. Almost makes me want to work on Dicty just to
go to the meetings!). (5) Dictyostelium Genomics. (6) Read the
Dicty News. (7) Franke Database of Dicty Literature. (8) Dicty Book of
Virtues (An interesting concept – to present a discussion of the
advantages of the organism for genetic, biochemical and evolutionary
research, that you can paste into a grant request! (9) Dicty Labs on the
Web. (10) Investigator Database (useful, but it does grab you and not
let you go unless you are an awfully rapid mouse clicker!). (11) Dicty
Listserv (I myself find Listservers annoying and much prefer a Bulletin
Board type of communication rather than receiving unwanted emails). (12)
Dictyostelium techniques (nice, but two of the protocol links are
currently broken). (13) Other Internet Biology Resources.
A well organized and informational site that provides much useful
information. This site really opened my eyes to recent research
on these organisms!
Giardia lamblia – A Model for Ancient Eukaryotic Genome Analysis
(http://www.mbl.edu/Giardia/index2.html):
A web site for the Giardia genome project. The rationale of
the project is well described, as is the sequencing strategy and the
enlightened rapid release policy. There are links to a
Giaridia-specific Blast server, BlastX annotations of gene
identifications, downloads of sequences in FastA format, Genome
sequencing statistics and publications by the sequencing consortium.
A very useful genome site for researchers on a fascinating lower
protist.
Woods Hole Astrobiology Institute Micro*Scope web site (http://www.mbl.edu/microscope/general/page_01.htm):
Astrobiology is a new field of research that yet lacks a subject
matter. However, studies of earthly microbes currently substitute for
studies of life on other planets. This site is still under construction
and already has over 400 excellent images of microbes. The links include
images of "Groups of Microbes", an alphabetical list of illustrated
microbes, microbes organized by habitat, classification of microbes, and
educational resources (two lectures so far). There is also a "Zeiss
downloadable image site" which has a number of high resolution images
indicating (I suppose) why you should buy a Zeiss microscope.
A site with great potential. I look forward with great
anticipation to seeing images of extraterrestrial microbes in the
future!
Larry Simpson
HHMI-UCLA, 6780 Mac Donald
Research Laboratories,
675 Charles E. Young Dr. S.,
Los Angeles, CA 90095- 1662,
USA
fax 1 310 206 8967;
e-mail simpson@hhmi.ucla.edu