The NSDL Scout Report for Life Sciences -- Volume 1, Number 19

October 4, 2002

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

In This Issue:




Topic In Depth


Patterns of Gene Expression in Drosophila Embryogenesis
A new image database of gene expression patterns in Drosophila embryogenesis is now available from the Berkeley Drosophila Genome Project (BDGP), a consortium of the Drosophila Genome Center. The BDGP team used "high throughput 96-well plate RNA in situ protocol to determine patterns of gene expression during embryogenesis for Drosophila genes represented in non-redundant sets of Drosophila ESTs DGC1 and DGC2." The entire set of image, microarray, and annotation data may be browsed or searched from this Web site. As of October 4, 2002, 1354 gene expressions have been documented with 25,263 digital photographs, with many more additions expected. This site also provides a useful FAQs page. [RS]
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AlgaeBase offers a free database of information on algae species around the world. This project is part of the Species 2000 initiative, created to enumerate "all known species of plants, animals, fungi and microbes on Earth as the baseline dataset for studies of global biodiversity." User may search the database for literature citations and photographs for algae identified by genus, species, or common name. The photographs, mostly of Irish species, are well referenced and often quite beautiful. Currently the seaweed data are most complete, but additional data are frequently added. Both the Web site and the database are straightforward and easy to use. [RS]
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InfoNatura: Birds and Mammals of Latin America
InfoNatura is provided by NatureServe, "a non-profit organization dedicated to developing and providing information about the world's plants, animals, and ecological communities." This Web site is a comprehensive source for conservation, distribution, and taxonomic information on over 5000 bird and mammal species in 44 Latin American and Caribbean countries. Taxonomic treatment of all species in the database "reflects standard references, and most species have been assigned a global conservation status rank." InfoNatura is updated three times a year to include "new data from refined geographic surveys, the latest taxonomic treatments, and any new conservation status assessments." Future versions of the database will include amphibian and reptile data. In addition to searching the database, users can click on Data Sources and Management to learn where InfoNatura data come from. [RS]
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PLANTS Threatened and Endangered Module
Offered through the Natural Resources Conservation Service of the US Department of Agriculture, the PLANTS Database Threatened and Endangered module (PLANTS T&E) now provides access to information on state and federally protected plants. Users have the following list-viewing options: the complete federal list; the federal list for one or more states; a state list; a state list for multiple states; and a federal and state combination list. Users may also search the database by plant family, genus, or common name. The Web site also provides related state and federal resource agency links for more information regarding plant protection laws and efforts. Conservation planners and researchers should take advantage of this convenient online resource. [RS]
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FishBase on the Web offers a free "relational database with information to cater to different professionals such as research scientists, fisheries managers, zoologists and many more." Developed at the International Center for Living Aquatic Resources Management together with the Food and Agriculture Organization of the United Nations and many other partners, FishBase is the online source for "all you ever wanted to know about fishes." This multi-featured Web site is frequently updated. Recent additions include a Life History Tool for calculating whole-body nitrogen and crude protein 115 content from wet weight and a new mapping tool that "allows zooming, point identification, different environmental layers, environmental boundaries and environmental forcasting [sic] for FishBase point data." Other features of this extensive Web site are too numerous to list. [RS]
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Photo Essays at the Missouri Botanical Garden
The research department of the Missouri Botanical Garden invites viewers to "travel with our botanists as they collect in different parts of the world, see some of the plants they collect, and learn more about the countries they collect in." Six polished photo essays are available for field work conducted in Gabon, Venezuela, the Republic of Georgia, the Cordillera de Condor region, and elsewhere. The photos display individually with descriptive captions and include more than just botanical subjects. Viewers may also access detailed information about each research project by following provided links. This Web site offers an entertaining, slicked-up look at botanical research in the field. [RS]
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CephBase [.pdf. RealPlayer, QuickTime]
CephBase is a collection of databases developed by the National Resource Center for Cephalopods at the University of Texas Medical Branch in Galveston. The Web site provides "taxonomic data, life history, distribution, images, videos, references and scientific contact information on all living species of cephalopods (octopus, squid, cuttlefish and nautilus) in an easy to access, user-friendly manner." The recently updated image database includes hundreds of well-referenced images that cover "all life stages, behavior, ecology, taxonomy as well as many other aspects of these amazing animals." The reference database contains over 5000 papers, some downloadable, with about 100 new entries added weekly. The site also features a database for cephalopod beak data organized by species. The video clips are worth watching for their entertainment value alone. [RS]
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Journal of Integrative Neuroscience [.pdf]
This Web site provides free access to an electronic version of the first issue of the Journal of Integrative Neuroscience (JIN), which debuted in June 2002. Published by World Scientific Publishing Co., JIN aims to "provide a dynamic forum for a synthesis of the brain sciences through the integration of neuroscientific phenomena, using new technologies that allow traversing multiple levels of neural organization, such as functional neuroimaging and specific databasing for neurosciences, and modeling." Users may also complete a Web form to receive a complimentary print copy of JIN, although specific issues cannot be requested. [RS]
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The Secret Life of the Brain [Flash, RealPlayer, Shockwave]
This Web site is the online companion to a five-part series about the human brain from PBS. With loads of fantastic interactive features, this site makes learning about the brain both fun and educational. One of the highlight of this site is the 3-D tour of the brain; users can rotate and zoom in or out on a model of the brain, clicking on areas of interest to learn their function. The drop-down menus on the same page allow users to quickly explore the brain by function or area. Other features of this Web site include timeline for the history of the brain; a segment that demystifies brain-scanning techniques; and a set of mind illusions, including a rather freaky one involving Abraham Lincoln. Visitors may also access overviews and video clips from each of the five episodes in the television series, which cover the baby, child, teenage, adult, and aging brain. A fascinating subject and an excellent Web site for any audience. [RS]
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Silent Invaders [.pdf, QuickTime]
A joint effort of the Interactive Media Science Projects at Florida State University and the Bureau of Land Management, US Department of the Interior, Silent Invaders presents a comprehensive and very visual introduction to invasive species in the US and Guam. Click on Introduction to view five QuickTime documentary-style movies that provide an overview of the topic. Other categories offer detailed information, photographs, and more movies addressing invasive plant and animal species, control measures, and prevention. Teachers may access a downloadable weed science primer from the Educator's Guide. The developers at Florida State University invite educators to take advantage of "the flexible framework -- clear, strong, and simple activity structures" provided by this Web site. With its many QuickTime movies, this site is best viewed with a high-speed connection. [RS]
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WhaleNet Blue Whale Data
This interactive educational Web site from WhaleNet provides a study guide to use with blue whale satellite tag data. WhaleNet is sponsored by Wheelock College, and the blue whale data set comes from the Mingan Island Cetacean Study, a "non-profit research organization dedicated to ecological studies of marine mammals." The study guide consists of a series of questions that guide students in analyzing and interpreting data. In the larger context, these questions uncover how satellite tag data provides valuable insight "into the natural history of the whales and will enable more intelligent and meaningful decisions which will increase the potential for recovery and for an improved existence in the shared marine environments around the world." Users of the Web site may also view blue whale tagging and biopsy movie clips. Links to a bibliography and additional resources are provided. [RS]
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Butterfly Lab [QuickTime]
This Web site comes from the Peggy Notebaert Nature Museum's Judy Istock Butterfly Haven, located in Chicago, Illinois. Designed for students in grades 7-12, Butterfly Lab offers online activities and materials covering butterfly anatomy, life cycle, behavior, and related topics. Detailed information is accompanied by colorful diagrams and photographs. Butterfly Lab also offers three offline activities involving butterfly anatomy, movement, identification, handling, and more. Students may submit their offline creations to be posted on the Web site. An audio feature allows users to listen to the Museum's director of biology discuss butterfly biology. The site includes a guide for teachers and a FAQ page. [RS]
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Two from the National Center for Case Study Teaching in Science
Experimental Design and Statistical Analysis: Bt, Lignin, and ANOVAs Lesson Plan [.pdf]
Teaching Notes [.pdf]
The National Center for Case Study Teaching in Science (NCCST) at State University of New York-Buffalo has recently added this lesson plan to its extensive collection. The NCCST aims to encourage the use of case studies in science courses, as they hold "great promise as a pedagogical technique for teaching science, particularly to undergraduates, because it humanized science and well illustrates scientific methodology and values." This particular lesson plan guides students in analyzing the abstract, methods, and results of a research paper about the lignin content of genetically modified corn, published in the American Journal of Botany. It is intended for use in a senior-level plant ecology course or a graduate level biostatistics course. The Teaching Notes Web site provides detailed background information and answers to lesson plan questions. The full article used for this case study is not available to nonsubscribers, but the lesson plan functions without it. [RS]
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Amphibian Embryology Tutorial [.jpeg, QuickTime]
Amphibian Embryology Tutorial, originally created to supplement Jeff Hardin's Introduction to Animal Development course at the University of Wisconsin-Madison, is "part of an ongoing project designed to implement multimedia and computer-based learning materials in the university undergraduate classroom." The tutorial is organized by major stages of development: Oogenesis and fertilization, cleavage, gastrulation, and neurulation. The Web site also includes an explanation of why we use amphibians to study development. The tutorial presents detailed explanations of each developmental stage and makes generous use of diagrams, photographs, and movie clips. This Web site would be a terrific resource for students wishing to review amphibian embryology outside the classroom at their own pace. [RS]
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Natural Selection Among Playing Cards
This no-frills Web site from the Evolution and the Nature of Science Institutes (ENSI) offers a lesson plan adapted from an article in The American Biology Teacher, April 2002. ENSI aims to "improve the teaching of evolution in High School Biology courses by encouraging teachers to teach evolutionary thinking in the context of a more complete understanding of modern scientific thinking." This particular lesson plan is designed to address a common misconception that arises when learning about natural selection -- that natural selection is random and non-cumulative and therefore cannot account for the evolution of novel, complex structures in relatively short periods of time. The lesson provided in this Web site offers students "an elegant, easy way" to understand the mechanism of natural selection by using playing cards and working in teams. A useful handout is provided, which includes a page of questions that could serve as the graded part of the exercise. [RS]
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The Tree of Life Web Project
The Tree of Life Web Project, originally created by biologists David and Wayne Maddison at the University of Arizona, is a "collaborative Internet project containing information about phylogeny and biodiversity (first mentioned in the December 6, 1996 Scout Report). Initially intended for use by biologists seeking taxonomic information, this Web resource has met with great enthusiasm from non-biologists, including middle and high school students, in the years since its creation. With frequent additions to the database, this Web site has expanded enormously since 1996. Very recent additions include a new page for Strepsiptera (twisted-wing parasites) and for Annelida (segmented worms). Life science educators and students should take advantage of this ambitious Web project as a learning tool. [RS]
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Hotspot: New Zealand [Flash, RealPlayer, Window Media]
This Web site supplements the October 2002 issue of National Geographic Magazine (last mentioned in the June 28, 1996 Scout Report). A number of entertaining multimedia features offer the visitor a look at the natural history of New Zealand, a biodiversity hotspot. Sights and Sounds of New Zealand, the highlight of the site, offers a seven minute presentation of beautiful photographs complete with commentary and bird calls. Users may also listen "to the booms, cackles, and trill of New Zealand's menageries of unusual birds," and view a bird image gallery containing photographs only available online. A bibiliography, links, map of New Zealand, and field notes from the article's author and photographer are also available. Sights and Sounds of New Zealand is best viewed with a high-speed connection, although a 56K connection can download this feature relatively quickly. [RS]
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The Accidental Scientist: Cooking [QuickTime, RealPlayer]
Another great Web site from the Exploratorium in San Francisco (last mentioned in the August 16, 2002 NSDL MET Report), The Accidental Scientist: Cooking is the first in a series of "Web-based projects focusing on the science behind everyday life." Offering a mind-boggling array of food-related information and activities, foodies and science-lovers alike should find this Web site extremely engaging. Life science-related material includes an exploration of taste and smell; the biological properties of meat; microbe action in pickling, fermentation, and leavening; and much more. The site's other features not directly related to the life sciences shouldn't be missed. Users can find recipes and cooking tips, fun projects, and live Web casts starting in November 2002 that explore the science and culture of cooking, "just in time for picking up cooking tips for the holiday season." [RS]
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Panda Central [.jpeg, Flash, RealPlayer]
Panda Central, "the exclusive Web home of Shi Shi, Bai Yun, and youngster Hua Mei," is provided by the San Diego Zoo. Visitors may view real time footage of pandas at the zoo with Panda Cam, have their questions answered at the Panda Facts page, or read up on each panda with Panda Profiles. And of course, no one should miss the features devoted to panda Hua Mei, who seems to have spent nearly every minute of her life in front of a camera since her birth at the San Diego Zoo in 1999. Visitors can watch video clips of Hua Mei from her birth onward, or view a slide show that chronicles her progress from a tiny unrecognizable lump to a "curious and precocious cub." The Web site has been recently updated to include a short piece about Hua Mei's third birthday, celebrated in August 2002. [RS]
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Gene(sis): Contemporary Art Explores Human Genomics
"Gene(sis) - the exhibition and the public programs - is the culmination of three and a half years of collaboration and cross-disciplinary activity involving a working group of artists, scientists, historians, bioethicists, representatives of the biotechnology industry and museum professionals engaged in an ongoing dialogue about the potential meanings and impact of current genomic research." This Web site offers visitors a close look at this cross-disciplinary project. Features include an online gallery of some of the pieces from the exhibition, intended to reflect recent developments in genomics and to demonstrate "the impact of genetics on artistic practice and on notions of the artist-subject." In joining two seemingly unlikely disciplines, this Web site offers an interesting exploration of the nexus of science and art. [RS]
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The American Museum of Natural History Congo Expedition [.pdf, Flash]
The American Museum of Natural History (AMNH) offers this multimedia introduction to the work of Herbert Lang and James P. Chapin, who led an AMNH-sponsored expedition to the Belgian Congo from May 1909- November 1915. The Web site provides visitors with a look at the natural history, geography, and people of the region as documented by Lang and Chapin. The highlight of the Web site is a five-minute narrated slide presentation about the expedition, best viewed with a high-speed connection. Visitors may also access an overview of the expedition that does not require the Flash plug-in. Also available are field notes and specimen data, photographs, images of watercolor sketches, anthropological data, relevant publications, and maps that reflect developing Western knowledge of African geography from 1562 to 1940. Much of this information has been entered into a searchable database. Other offerings include an extensive reference page (containing links to each publication), a searchable GIS map of Africa, a gallery of stereographic images (viewers may request a free pair of 3-D glasses), and more. In all, this multi-featured Web site is both interesting and entertaining, and offers visitors a sense of what the field of natural sciences was like in the early 20th century. [RS]
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Harvest of Hunger
The University of Wisconsin's Why Files (first mentioned in the August 9, 1996 Scout Report) has a recent in-depth feature that explores issues surrounding the creation of new agricultural plant varieties, with an emphasis on genetic engineering. The Web site consists of straightforward pages of text and photographs that relate the past, present, and possible future of plant breeding and genetic engineering. Visitors may click on numerous links to access related Why Files stories or relevant information from elsewhere. The site also contains a bibliography compiling paper and electronic references for anyone wishing to learn more about the topic. In all, this Web site quickly but effectively conveys a sense of the questions and concerns raised by this topic. [RS]
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The Complete Morris's British Birds 1891
Individually produced by Ash Midcalf, this Web site contains digitized images from the Reverend Francis Orpen Morris's A History of British Birds, published in 1891. Artist-naturalists like Morris and Audubon created painstakingly true-to-life depictions of the planet's flora and fauna in the days before reliable photography. Visitors to this Web site can browse through pages of thumbnails, choose from the complete list of images, or use the search feature to view any of the 394 prints available. A page for Links is provided, but currently lists only one. [RS]
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The Chesapeake Bay Program [.pdf]
This Web site is the online presence of the Chesapeake Bay Program, "a unique regional partnership that has led and directed the restoration of the Chesapeake Bay." The site offers a wealth of information regarding the region's flora and fauna, habitats and ecosystem processes, restoration efforts, current events, and much more. For instance, click on Animals and Plants to access pages and pages of well-organized information about the area's shellfish, reptiles, mammals, insects, bay grasses, invasive species, and others too numerous to list. Each page contains a convenient glossary for important terms and links to related resources. Chesapeake Bay Program publications are also provided, although only some are available for immediate download. In all, this is an informative and easy-to-use Web site that even those not familiar with Chesapeake Bay should find interesting. [RS]
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Topic In Depth

Restoration Ecology
1. The Society for Ecological Restoration
2. The Center for Restoration Ecology
3. A National Strategy to Restore Coastal and Estuarine Habitat
4. Nature/ Ecology at the Fermi National Accelerator Laboratory
5. Kissimmee River Restoration
6. RESTORE: The North Woods [Flash]
7. The Wildlands Project
8. Reconstructing a Prehistoric Scottish Woodland
While not a panacea, the emerging field of restoration ecology provides an important tool for environmental conservation and contributes greatly to our understanding of ecology.

The first Web site is the home page of the Society for Ecological Restoration, offering a good starting point for exploring this relatively new discipline (1). The next site (2) provides an overview of the University of Wisconsin's Center for Restoration Ecology, "the first comprehensive, interdisciplinary research team assembled to advance the science and technology of ecosystem restoration." The National Oceanic and Atmospheric Administration outlines its plans for coastal and estuarine restoration in this Web site (3). The Fermi National Accelerator Laboratory in Illinois has implemented one of the largest tallgrass prairie restorations to date (4). The Kissimmee River Restoration Web site (5) provides a detailed look at this incredibly ambitious dam removal and wetland restoration project in Florida. The next Web site (6) offers a visually-attractive introduction to the restoration efforts of the nonprofit organization RESTORE, focusing on the forests of Maine. The Wildlands Project, another restoration-oriented nonprofit organization, describes its vision of ecosystem conservation in this Web site, which includes a personal brief from distinguished biologist E. O. Wilson. (7). The Wildwood project of the Scottish organization Carrifran offers an interesting contrast to restoration efforts in the US, as much of Scotland has been denuded of its original forests for thousands of years (8). [RS]
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