The NSDL Scout Report for Life Sciences -- Volume 2, Number 8

April 18, 2003

A Publication of the Internet Scout Project
Computer Sciences Department, University of Wisconsin-Madison

In This Issue:




Topic In Depth


BioMedNet: Neuroscience Gateway
The Neuroscience Gateway from BioMedNet has recently gone live, offering "expertly selected content from leading publications" (all published by Elvesier), including Neuron,Neurosciences, and others. The Neuroscience Gateway, one of a growing number of BioMedNet Web portals for the life sciences, is updated every two weeks to bring neuroscience researchers the latest field-related scientific and feature articles, research updates, book reviews, and much more. All resources are available free of charge to any user after registering with BioMedNet (a quick, simple process). Updated every two weeks, the Neuroscience Gateway is currently focused on "translational neuroscience," and will offer free access to full-text articles from a recent special issue of Brain, Behavior and Immunity until the next update." [RS]
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Melastomataceae of the World
This Florida Museum of Natural History of Web site provides a convenient, centralized clearinghouse for information on the Melastomataceae. Created to promote research on this common yet understudied family of tropical plants, the Melastomataceae of the World Web site provides images and background information, a phylogenetic overview, links to related research projects, contact information for melastomatologists working around the world, bibliographic references, links to useful online databases, and much more. Well organized and remarkably comprehensive, this Web site really does a service to Melastomataceae research. [RS]
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Traditional Ecological Knowledge Prior Art Database
The Traditional Ecological Knowledge Prior Art Database (TEK*PAD) "is an index and search engine of existing Internet-based, public domain documentation concerning indigenous knowledge and plant species uses." TEK*PAD, a multi-organization collaboration offered through the American Association for the Advancement of Science, provides links to taxonomic data, ethnobotanical information, academic abstracts and articles, and other resources intended to facilitate research on traditional ecological knowledge. The database itself may be searched easily by keywords, plant names, medicinal application, geographical region, or cultural/ ethnic group. The Web site also includes recent news articles and other features, such as the Biopiracy Hot List. Even those not actively involved in ethnobotanical research should find the TEK*PAD Web site worth exploring. [RS]
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Plant Cell Imaging [QuickTime]
The Department of Plant Biology at the Carnegie Institution of Washington offers a fascinating collection of plant cell images created using fluorescent molecular tags (isolated from a species of bioluminescent jellyfish) and fluorescence microscopy. Visitors will find an extensive collection of movies presenting different cell types, subcellular components, and dynamic cellular processes in the model plant Arabidopsis thaliana. The Web site also includes detailed equipment and protocol information, as well as links for tools, software, and other related Web sites. Visitors are encouraged to view the site and its content with a Macintosh, if possible. [RS]
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BioChipNet: The Informational Website on BioChip Technologies [.pdf]
The BioChipNet database, maintained by researchers at the University of Tbingen in Germany, offers a "comprehensive information platform on microarrays and related fields." The BioChipNet Web pages offer a mountain of microarray-related resources, including profiles of companies and institutions engaged in biochip technology, links to PubMed articles, announcements of upcoming meetings and conferences, a detailed glossary, and more. Researchers and commercial interests alike should find BioChipNet and its conveniently centralized catalog of microarray resources of use. [RS]
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Bermuda Biological Station for Research
This Web site contains the homepage of the Bermuda Biological Station for Research (BBSR), established "to conduct research and science education of the highest quality from the special perspective of a mid-ocean island." The site offers detailed overviews of BBSR research initiatives, including a number projects in the life sciences: marine biodiversity, the ecosystem functions of coral reefs, ocean genomics, aquaculture, ecotoxicology, and pollution studies. Visitors can also go on a virtual tour of the research station. Altogether, this Web site offers a quick yet engaging introduction to research at the BBSR. [RS]
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NZFUNGI: New Zealand Fungi
Manaaki Whenua Landcare Research -- "New Zealand's foremost environmental research organization" -- presents NZFUNGI, a free database for information on the systematics, conservation, pathology, and ecology of New Zealand's fungi. Integrating a number of pre-existing Landcare Research databases, NZFUNGI contains botanical, bibliographic, and curatorial information for thousands of New Zealand fungi species. Although the Web site currently lacks a search help page, using the database is fairly self-evident, and Landcare Research will welcome any emailed search questions. [RS]
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Genomes to Life Contractor-Grantee Workshop I [.pdf]
This Web site contains the proceedings of the Department of Energy's Genomes to Life (GTL) first annual Contractor-Grantee Workshop, held in February 2003. The GTL program integrates "genomic data and high-throughput technologies for studying the proteins encoded by the genome to explore the amazingly diverse natural capabilities in microbes," with exciting applications for bioremediation, energy production, and global climate change mitigation. The conference proceedings cover a range of related topics presented by experts from universities and research centers throughout the US, and may viewed online or downloaded in regular or high-resolution sizes. [RS]
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The Temperate Rain Forest Canopy of the Northwest [.pdf]
Students and teachers can virtually explore the canopy of the temperate rainforest in this Web site from the faculty Web site of canopy biologist Nalini Nadkarni at Evergreen State College in Olympia, Washington. The Web site includes six downloadable activities for grades 4-12 covering canopy hydrology, structure and ecology, a tardigrade lab, and more. The site also offers an interactive image for learning about 18 plants and animals that live within the canopy layers of a temperate rain forest; the Web pages provided for each organism include detailed descriptions and links for further information. Other features include instructions for making leaf and bark rubbings, a poetry writing exercise, and a number of Web links for information on recycling and sustainable forestry. [RS]
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PBS Newshour Extra: AIDS Today
AIDS Today, a lesson plan for grades 9-12 form PBS Newshour Extra, "engages students in learning about the AIDS epidemic and focuses them on the importance of HIV prevention, at home and abroad." The lesson plan requires two 90-minute periods to complete and calls for nothing fancier than Internet access for materials. Links to PBS Newshour story transcripts are provided for use with the lesson plan, which consists primarily of questions for class discussion as well as small group and individual learning activities. [RS]
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AskERIC: Parts of a Spider
This Web site from AskERIC, the Internet-based service for the Educational Resources Information Center (U.S. Department of Education), contains a simple lesson plan for preschoolers and kindergarteners created by Cara DiFrango of the University of Pittsburgh at Johnstown. With clay, paint, a short play, and a reading of "Are You a Spider?" by Judy Allen, students will have fun learning about the parts of a spider in two 30-minute sessions. The Web site includes a short vocabulary list and ideas for using computers with the lesson plan. [RS]
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Science NetLinks:Growing Vocal Cords [RealPlayer]
This Science NetLinks Web site contains an interesting lesson plan that has students explore the emerging field of tissue engineering, looking particularly at tissue engineering in the repair of scarred vocal cords. The lesson is based a 90-second feature from Science Updates, a radio program from Science NetLinks presenting current scientific research. Students listen to the program, which features an interview with Julie Andrews (who suffered vocal cord damage in 1997), and then test their understanding of tissue engineering and stem cell research using the provided questions. The site also includes Web links for further information. Altogether, this lesson plan offers an interesting look for covering stem cell and related research in the classroom. [RS]
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Mike Johnson Marine Natural History Photography [QuickTime]
Mike Johnson, professional underwater photographer working in southern California, offers a fantastic collection of underwater and topside nature photography free of charge for noncommercial use. The image gallery includes gorgeous photos of blue whales, ocean sunfish, pelagic crabs, stingrays, marine fossils, and other marine animals of southern California and the northern part of Baja California. QuickTime video footage of blue whales is also available. Students may use any images from this Web site for written reports and classroom presentations if properly credited, while researchers and instructors may also use them for purposes covered by Fair Use under US copyright law (does not include use for Web sites). [RS]
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Buscope [DepthCharge, Steroscope]
The Bugscope project, offered through the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign, allows K-12 classrooms to remotely operate a scanning electron microscope (SEM) in real time from a classroom computer to create incredibly cool images of insects and other "bugs" at high magnification. Detailed instructions for scheduling a session and using the SEM are provided. Classrooms design their own experiments and mail their own specimen(s) to Bugscope, which provides the imaging services completely free of charge. The only equipment required on the part of the classroom is a computer with Internet access. Users can also visit Bugscope's fantastic image collection: a 3D image gallery (requires Stereoscope Java applet or DepthCharge plugin) and a set of 42 psuedo-color stereograms for an up-close look at spider fangs, mouse stomach, and even "fly booty." [RS]
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Reciprocal Net: Common Molecules Collection
Part of the Common Molecules Collection, this set of 3D biochemical molecule images is an educational feature from Reciprocal Net, a Web portal for crystallography research funded by the National Science Foundation and part of NSDL. The Common Molecules Collection currently offers a number of image galleries, but only a couple -- including the biochemical molecules set -- with direct life sciences application. Users can view and rotate a 3D image for each molecule provided (organized by amino acids, hormones, and nucleosides), accompanied by a brief explanation and other particulars such as chemical formula. It's a great tool for visual learners and a fun Web site to visit just for the 3D effects. [RS]
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Cuyahoga Valley Online Alphabet Book
This National Park Service Web site for contains an appealing online alphabet book based on the plants and animals found in Cuyahoga Valley National Park, located near Cleveland and Akron, Ohio. The alphabet book offers great photos (mostly of animals) with personable, friendly captions from A (New England Aster) to Z (a baby opossum catching some "ZZZs"). It's geared toward little kids, but fun for not-so-little kids too! [RS]
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Steinhart Aquarium [.pdf]
A visit to the Web site of the California Academy of Sciences Steinhart Aquarium must be nearly as good as a trip to the aquarium itself. The site offers a number of engaging features for exploring the aquarium and its resources. For example, clicking the seahorse photo on the main page will call up well-presented background information about seahorses and pipefish, related Web references, and a number of great photos. The Web site also provides information about overfishing and sustainable seafood harvest, including a downloadable Seafood Buyer's Guide. Other features include a penguin cam where visitors can watch live Web feeds of the aquarium's black-footed penguin colony, recent ocean news, a guide to exploring and protecting California's tide pools, and more. On the whole, any visitor should enjoy this virtual visit to the Steinhart Aquarium. [RS]
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Two from Lawrence Berkeley Laboratory
A New Branch on the Tree of Life
Mice Offer Lessons on Aging
The Lawrence Berkeley Laboratory's Science Beat offers interesting feature articles about research from Berkeley lab and partner organizations. The two Web sites above contain recent Science Beat stories. The first article describes new findings that the insect-like collembolans, a group commonly thought to have given rise to true insects, are not closely related to insects at all and in effect constitute a newly discovered branch of the phylogenetic tree. The second article offers a fascinating look at aging research utilizing transgenic mice -- an inquiry into "the genetic roots of aging in everyone." Both articles include Web links to related material from the institutions participating in these research projects, as well as links to academic articles from the journal Science (not available without paid subscription). [RS]
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AARP: Evaluating Health Information on the Internet
The American Association of Retired Persons (AARP) offers this informative Web site on evaluating health information found on the Internet. As the introduction explains, "the sheer breadth of information in cyberspace can be overwhelming," and "separating reliable from questionable heath information can be a significant challenge." Fortunately, AARP provides a valuable crash course on assessing the quality of online sources, outlining the issues that require a healthy dose of consumer skepticism. The site also provides useful links for further information, such as the US Food and Drug Administration guide to buying pharmaceuticals online and Medline Plus from the National Library of Medicine. [RS]
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Real Men. Real Depression. [.pdf]
The National Institute of Mental Health (NIMH) presents this tremendously comprehensive Web site as part of an information campaign designed to increase public awareness of depression in men, who "are less likely than women to recognize, acknowledge, and seek treatment for their depression" even though an estimated six million men suffer from this illness in the US alone. The main feature of the campaign and this companion Web site is a series of candid, personal stories from men describing their experience with depression. Participants include a retired US Air Force First Sergeant, a firefighter, a writer, a publisher, a national diving champion, a lawyer, a police officer, a student, and others. In addition to their stories, which may be read or heard as audio clips, the Web site offers a wealth of information and resources on depression for sufferers as well as for their friends and families. A number of downloadable publications on the subject are also available, which may also be ordered through the mail free of charge. [RS]
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NOVA: Deep Sea Invasion [Flash]
This is the companion Web site to "Deep Sea Invasion," a PBS NOVA documentary broadcast April 1, 2003. The program follows marine biologist Alexandre Meinesz and his scientific detective work to explain the rampant spread of the tropical alga Caulerpa taxifolia through the Mediterranean and his struggle to instigate control efforts. The features of this Web site include a timeline chronicling the invasion, an article by Meinesz on the impact of invasive species, another article addressing strategies for controlling invasives, and an interactive quiz in which users match up species with their invasive characteristics. With interesting material covering a range of ecological topics, this Web site should be of interest to any reader. [RS]
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National Geographic Magazine: Jane in the Forest Again
In this Web site from National Geographic magazine, readers can follow the adventures of Jane Goodall, "the famed primatologist [as she] meets the chimpanzees of Congo's Goualougo Trainge, animals so isolated they have no fear of human -- at least for now." In addition to a substantial excerpt from the print article (by David Quammen), the Web site offers a number of Web-only items, including a number of engaging multimedia features such as video footage of tool-wielding chimps. Other features include field notes from photographer Michael Nichols, an online-only image gallery (including the photographer's technical notes), related Web links, and more. [RS]
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Nature lovers and photographers are invited to upload and share their favorite wildlife photos in this straightforward, privately hosted Web site, a place where "viewers from around the world can see what animals, plants, and landscapes look like in other places." currently features a modest collection of images grouped by class (all vertebrate): birds, fish, mammals, and reptiles. Future versions of this Web site will be organized by taxonomy and by geographic location, with plans to map out territories and migration routes of each species. This could be an interesting site to watch as contributions from visitors start to increase. [RS]
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National Wildlife Health Center: Chronic Wasting Disease [.pdf]
The US Geological Survey's National Wildlife Health Center offers this no-frills Web site for information on chronic wasting disease (CWD). The introductory material provides a condensed background to the disease and the still problematic CWD outbreak, followed by an extensive collection of Web links for more detailed information. Many links lead to related USGS Web sites. The site also provides a link to a full-text academic article on transmissible spongiform encephalopathies (including, of course, CWD). Graphic version of this Web site not available. [RS]
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Topic In Depth

1. Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources
2. NIGMS: Medicine for You
3. Medicine and the New Genetics
4. Chemical and Engineering News: Pharmacogenomics
5. BioIT World: The New, New Pharmacogenomics
6. NIGMS: Medicines by Design
7. Pharmacogenomics: The Promise of Personalized Medicine [.pdf]
8. The Pharmacogenomics Journal
The first Web site (1) from the National Center for Biotechnology Information offers a brief introduction to pharmacogenomics, a new science that "examines the inherited variations in genes that dictate drug response and explores the ways these variations can be used to predict whether a patient will have a good response to a drug, a bad response to a drug, or no response at all." This Web site defines pharmacogenomics as separate from pharmacogenetics, but explains that the two terms are used interchangeably in most cases. The second Web site contains an online brochure about pharmacogenomics from the National Institute of General Medical Sciences geared toward a general audience (2), and is also available in Spanish. To put the emerging field of pharmacogenomics in the overall context of genetics research, check out the next Web site from the Human Genome Project (3), which provides an overview of medical genetics. The next two Web sites contain in-depth articles about pharmacogenomics issues. The first, a cover story from Chemical and Engineering News (C&EN), delves into pharmacogenomics and the concept of personalized medicines, and also profiles some of the pharmaceutical and biotechnology companies active in this field (4). This site also includes links to related C&EN articles. The second article, from BioIT World, describes in detail how most pharmaceutical companies currently concentrate on weeding out potentially dangerous compounds rather than developing personalized drugs (5). Readers who would like to learn how the body metabolizes drugs (and thus gain a better understanding of what pharmacogenomics research addresses) should take advantage of the following Web site (6), also from the National Institute of General Medical Sciences. The next Web site contains an academic (but not scientifically obscure) article from PharmSci, a publication of the American Association of Pharmeceutical Scientists (7). The article, titled Pharmacogenomics: The Promise of Personalized Medicine, presents a comprehensive account of pharmacogenomic research, including historical perspective. Web links to PubMed documents for most of the article's references are provided. The last Web site, from the Nature Publishing Group, offers users a free online sample of The Pharmacogenomics Journal (8), published in 2003. [RS]
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