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20 Oct 2006
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Bioinformatics Home Base
Biologists who lament, "So many databases, so little time," should check out this portal from the University of Pittsburgh in Pennsylvania. The site provides brief descriptions of more than 1500 free bioinformatics databases and tools in categories such as immunology, genomics, and RNA. If you're looking for data on how pathogens alter gene activity in immune cells, for instance, follow the link to the Macrophage Expression Atlas in the U.K. Or the site can help you sift through the more than 70 databases with information on plant genes and proteins.
6 Oct 2006
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Time for a Close-Up
A freshwater shrimp (Macrobrachium amazonium) goggles at the camera through a square pupil. The shot by photographer Alex Griman of São Paulo, Brazil, nabbed one of the top places in this year's Small World contest, sponsored by the camera company Nikon. Held annually since 1974, the competition showcases photographic artistry through the microscope. Visitors can browse a gallery of this year's best submissions or check out previous winners. Peruse the backgrounders if you're curious about winning techniques such as stereomicroscopy, which Griman used to capture the shrimp image.
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Bioinformatics for Everyone
Want a rundown on the differences between the UniProt, PROSITE, and PDB protein databases? Wondering how to find a paper that doesn't show up in PubMed? Try a session with the 2can primer from the European Bioinformatics Institute (EBI) in Hinxton, U.K. The site guides newbies and intermediate users who want a little help through a host of databases, online tools, and additional resources from EBI and other institutions. In the databases section, for example, you can learn when you might need PROSITE. It's useful for analyzing new proteins because it organizes molecules by characteristic sequences, or motifs, that can point to their functions. The tutorials pages offer detailed how-tos on several EBI programs.
14 July 2006
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Immunologists of NIH, Unite!
Immunologists in the National Institutes of Health's (NIH's) intramural program are scattered among more than a dozen institutes. The new hub Immunology@NIH connects researchers in far-flung labs and helps outside scientists track down potential collaborators. The site holds a directory of some 150 NIH scientists who are probing the immune system. Visitors can also browse a listing of training opportunities or dig into a video archive that houses 4 years of immunology seminars by NIH staff members and other researchers.
9 June 2006
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Telltale Spots
ProMAT is a free program for analyzing protein microarrays. Relatives of DNA chips, the microarrays can help researchers identify proteins lurking in a drop of blood or a particular cell type and measure their concentrations. The software, which works for ELISA microarrays, can also help users gauge the reliability of their data. To download it, visitors need to register by e-mail with the program's creators at the Pacific Northwest National Laboratory in Richland, Washington.
12 May 2006
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Thinking Like a Tumor
Inside Cancer, a new primer from the Cold Spring Harbor Laboratory in New York, explains the basics of tumor biology with a snazzy mix of text and multimedia. Start with the Hallmarks of Cancer section to hear experts such as Robert Weinberg of the Massachusetts Institute of Technology talk about the abilities a cell needs to spawn a tumor, which include dodging the immune system and thwarting suicide pathways. In the action-packed Pathways to Cancer animations, visitors wend through a cell's cluttered interior and plunge into nuclear pores to see how the signaling systems that normally manage division go awry. Other sections explore cancer epidemiology and new treatments.
24 February 2006
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Gene-o-Matic
This new program from the Johns Hopkins Medical Institutions in Baltimore, Maryland, is a timesaver for scientists who craft DNA sequences for genetic engineering or to decipher gene functions. Users key in a protein sequence, and GeneDesign specifies a DNA blueprint that researchers can synthesize themselves or order from a company. GeneDesign lets users customize their creations for a particular vector--a DNA snippet that ferries the sequence into cells--and for the organism they are studying.
16 December 2005
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Avoid Lab Mix-Ups
Nested or real-time PCR? Western, Southern, or Northern blotting? Newbies struggling to keep genomic methods straight can get help at this primer written by biologist Malcolm Campbell of Davidson College in North Carolina. Methods for Genomics isn't a lab manual but instead briefly explains more than 50 widely used techniques and pieces of equipment. With diagrams and animations, the site helps students grasp lab staples such as electrophoresis and more advanced methods such as the Cre/loxP recombination system for deleting specific sections of DNA. The content ties in with a text Campbell uses in his classes, but it also works as a standalone resource.
7 October 2005
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Home Base for Microbes
You'd expect microbes to be high on the research agenda at the National Institutes of Health, but many other federal agencies sponsor or conduct investigations of the bugs, from the Department of Defense to the National Institute of Standards and Technology. Visitors can discover more about these efforts at The Microbe Project. The new portal offers a synopsis of each agency's microbiological research, often providing links to projects, databases, and other resources. The site also furnishes news and an education section, which includes information on fellowships and mentoring programs.
30 September 2005
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Molecular Pick Ax
Knocking out genes is one way to decipher their function. Another method that's gaining popularity is chemical genomics: using small molecules to tweak biochemical pathways. To help researchers sift candidates for these experiments, the site ChemMine from the University of California, Riverside, profiles more than 2 million compounds from commercial suppliers and public databases such as the National Institutes of Health's PubChem. ChemMine's selling point is its many tools. You can track down molecules by structure, chemical properties, and activity; tease out similar compounds; and cluster the results by similarity.
23 September 2005
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A Bigger BLAST
The new site SEQUEROME supplies a suite of tools for analyzing the results from BLAST searches of DNA and protein sequences. At your fingertips are buttons that allow you to identify where particular DNA-chopping enzymes will cut the sequence or determine what amino acid string it codes for.
InstaSeq, another offering from the same group at Georgetown University in Washington, D.C., scans the Web as well as gene databases for particular DNA, RNA, or protein sequences. The tool can rummage through Microsoft Word files,
PDFs, and Web pages.
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Profiles in Science: Secrets of the Phage
After scraping through his chemistry and biology classes, Salvador Luria (1912-1991) only entered medical school in his native Italy because of parental pressure and "my own lack of alternative inclinations." Luria caught the science bug, though, and some 40 years later shared the 1969 Nobel Prize in physiology or medicine for pioneering work on viral genetics. The latest installment in the U.S. National Library of Medicine's Profiles in Science series looks back at his life and career. He was one of the first researchers to harness bacteriophages--viruses that attack bacteria--to probe the mechanics of inheritance. At the site, you can browse photos, letters, selections from Luria's laboratory notebooks, and other documents. For example, you'll find his breakthrough 1943 paper with biophysicist Max Delbrück that solidified the then-controversial idea that bacteria have genes.
12 August 2005
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Fun With Genetics
Dive into a human skin cell and zoom in on a loop of DNA. Quiz an expert about the genetics of diseases such as lupus. Those are two of the activities you can try at Understanding Genetics from the Tech Museum of Innovation in San Jose, California. Interactive exhibits let you explore topics such as eye color inheritance and whether the produce in your refrigerator could be genetically modified. The museum's on-call geneticist discusses issues in the news and answers questions from readers, such as whether a vegan diet reduces your tolerance for milk. Probably not, because the gene for lactase, the enzyme that breaks down milk sugar, naturally shuts off as most people age, regardless of diet. But not drinking milk for a while might eliminate bacteria that help digest it.
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Snooping for SNPs
The genome's typos, single-nucleotide polymorphisms (SNPs), are one-letter changes in DNA that can signal susceptibility to diseases. WatCut from the University of Waterloo in Canada helps pinpoint SNPs in DNA samples. Users enter a SNP-containing DNA sequence, and WatCut identifies restriction enzymes that will chop the segment. The site can also hunt for silent mutations that allow a restriction enzyme to slice a sequence but that don't change the amino acids the sequence codes for.
5 August 2005
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Cells Gone Wild
Hungry tumor cells send out for dinner, releasing molecules that spur blood vessels to grow toward them. Learn more about the insidious ability--known as angiogenesis--and other aspects of cancer biology at this tutorial from lecturer Gregg Orloff of Emory University in Atlanta, Georgia, and contributors. The site is aimed mainly at cancer patients and health care workers but includes plenty of information for students. With an abundance of animations and diagrams, CancerQuest's 13 chapters plumb subjects such as the control of cell division and how defective genes bollix the delicate process. Visitors can also read up on clinical trials and experimental therapies, such as poisons that target only brain cancer cells carrying a particular surface receptor. Orloff is overhauling the site and will soon add new graphics and a timeline of cancer discoveries.
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Deconstructing Viruses
If you're hunting for tools to analyze virus genomes and proteins, drop by The Viral Bioinformatics Research Center, created by Chris Upton of the University of Victoria in Canada. The site holds sequences for hundreds of viruses in 11 families, such as the Filoviridae, which includes the notorious Ebola virus. You can parse the data using 10 Java tools; for example, the Base by Base program lets users compare viral genome sequences one nucleotide at a time. The site also offers background on the different families, describing their structures, life cycles, and how they hijack cellular activities. To learn more about some viral illnesses, download chapters from an infectious disease text.
20 May 2005
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Death by Design
Every day millions of our cells kill themselves and biologists say, "Thank goodness." Known as apoptosis, this methodical self-slaughter helps defend against cancer, lets the brain make the right connections during development, and contributes to many other body activities. Newbies can absorb the basics of the process with this pair of tutorials.
Videos of suicidal cells and images such as the "death receptor" add panache to the primer* by postdoc Phil Dash of St. George's Hospital Medical School in London. Embedded in a cell's membrane, the receptor picks up the suicide signal and unleashes enzymes called caspases, which help orchestrate the cell's demise. Learn about the survival pathways that spare cells and read about diseases in which control of apoptosis falters at this site from graduate student Alasdair Laurie of the University of Leeds, U.K. Too little apoptosis lets tumors run amok, and too much depletes needed cells in Huntington's disease and AIDS.
13 May 2005
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A Killer Remembered
Americans were so worried about polio in the early and middle 20th century that some towns forbade travelers under 16 years old from entering, fearing they might be carrying the disease. At Whatever Happened to Polio? you can look back at those nervous days and learn about the vaccines that helped stamp out polio in the United States.
The new Web site, which accompanies an exhibit at the Smithsonian Institution, marks the 50th anniversary of the polio vaccine. It offers period photos, audio clips from polio survivors, and other resources that chart the disease's wrenching impact on society and families. For instance, newly diagnosed children were often quarantined for up to 14 days, followed by several weeks of limited contact with their parents. Technologies of the day included cumbersome iron lungs that helped paralyzed patients breathe. You can also learn about Jonas Salk's and Albert Sabin's vaccines. Salk introduced his vaccine first, but Sabin's, which relied on a weakened virus rather than an inactive one, was more widely used. A final section looks at current efforts to eradicate polio from the few countries where it remains.
22 April 2005
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Structural
Biology Starter Kit
So-called BLAST searches and fancy 3D molecular graphics may be a snap for veterans, but beginners often need help with the programs. Students and teachers can beef up their structural biology skills at The Molecular Level, a primer from chemist Gale Rhodes of the University of Southern Maine, Portland. Users can bone up on protein structure while learning to use the molecular modeling software DeepView. Another tutorial introduces 10 bioinformatics staples, including the sequence searcher BLAST and the protein analysis tool kit ExPASy. The site offers practice problems, and for the forgetful, there's an organic chemistry refresher.
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Smarter Searching
Even if you judiciously choose key words and skillfully deploy "ands" and "nots," searching a bibliographic database can return a torrent of hits or skip the paper you want. Researchers looking for an alternative way to bore into the Caenorhabditis elegans literature can glide over to Textpresso, a search engine from the operators of the nematode compendium WormBase.
Most bibliographic tools only scan abstracts. But Textpresso digs into the full text of more than 5000 nematode articles, along with some 18,000 abstracts from meetings, the Worm Breeder's Gazette, and other sources. And Textpresso lets you narrow your search by categorizing key words and specifying their functions and relationships to other terms. For instance, instead of trawling for all papers on the gene daf-2, which governs worm longevity, you can net only publications that record daf-2 activity in particular types of cells or that identify genes it interacts with. The site includes a similar search engine for the fungus Neurospora crassa and prototypes for fruit flies and papers from the Journal of Neurobiology. And other teams have launched Textpresso-based libraries for several model organisms, including yeast.
15 April 2005
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On the
Defensive
Signs of our protracted struggle against pathogens show up in our genome--up to 10% of our genes may help build or operate body defenses. Learn more about the molecular and genetic underpinnings of the immune system in this primer written by medical student Daniele Focosi of the International Centre for Genetic Engineering and Biotechnology in Trieste, Italy. Packed with links and original pages, Molecular Immunology is an outline-style guide aimed at upper-division college students and above. Readers can start by touring our border defenses, learning about, say, the 20 varieties of gooey mucin molecules that trap pathogens trying to sneak in through the nose, mouth, and other entryways. Other topics include the origin of infection-fighting cells such as the T cell and the immune systems of fruit flies and other model organisms.
18 March 2005
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Microbial Get-Together
This new clearinghouse from the U.S. Department of Energy can help researchers analyze the deluge of DNA data on microorganisms. Integrated Microbial Genomes stashes nearly 300 draft or completed genome sequences from
archaea, bacteria, and other bugs, along with tools for sifting through the data. Visitors can get acquainted with all 2526 protein-coding genes carried by the marine cyanobacterium
Synechococcus, for example. Besides basic information about the gene, its protein, and its function, you can summon diagrams illustrating which biochemical pathways the gene influences. Browsing tools make it easy to pinpoint similar genes in different organisms and compare them side by side.
25 February 2005
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After the Double Helix
"I have never seen Francis Crick in a modest mood," James Watson declared in his controversial book The Double Helix. Regardless of whether the characterization was accurate, Crick (1916-2004) had plenty to be immodest about. As you can see at this new exhibit on his life from the U.S. National Library of Medicine, Crick's contributions went far beyond co-discovering the structure of DNA.
After helping set the research agenda for molecular biology's early years, Crick at age 60 launched a new career as a neuroscientist, theorizing about questions such as the origin of consciousness and the function of rapid eye movement sleep. Along with a biography that follows his professional zigzags, the site holds letters, papers, photos, and other memorabilia from a collection cached at the U.K.'s Wellcome Library. You can peruse an early sketch of the double helix, for example, or read a letter from chemist Linus Pauling chastising Crick for including too few hydrogen bonds in a paper on DNA. Also included is a 1979 composite photo showing Crick's animated lecture style.
28 January 2005
Teachers looking for just the right illustration to clarify a microbiology lab or lecture might want to visit the Microbe Library. Since last reviewed by NetWatch (9 June 2000, p. 1699), the educational site from the American Society for Microbiology has begun charging for course materials, but most of the visuals remain free. Check out more than 350 photos, diagrams, and videos from microbial mug shots to animations that explicate biological processes such as gene regulation and DNA repair. Tutorials can help students master tools and techniques such as acid-fast staining, used to identify bugs such as tuberculosis bacteria that shrug off traditional dyes. Included are stills which come from an animation that shows how a coated virus infiltrates an animal cell.
24 December 2004
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Genome Speed-Reading
A free program from the Broad Institute in Cambridge, Massachusetts, can help researchers locate genes and determine their functions in freshly sequenced genomes. Known as Argo, the new software makes it easy to compare notations about DNA landmarks, such as segments that might code for a piece of a protein, identified by automated genome-parsing programs. Argo-nauts can zoom in on these features and craft hypotheses about how they mesh to form a working gene. Another feature lets visitors analyze sequences from different species side by side.
3 December 2004
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Google for Academia
As if you weren't spending enough time Googling, now the search engine offers another reason to loiter there: a bibliographic tool aimed at scientists and other researchers. Google Scholar, a beta version of which launched last month, trolls for articles, reports, and other documents from publishers, universities, professional societies, and abstract databases such as PubMed. Almost all top scholarly publishers have agreed to let Google index their sites, says principal engineer Anurag Acharya, including the publishers of Science and Nature.
Instead of the list of Web sites, an author search for Francis Crick returns a roster of his works, beginning with a citation for the 1953 paper on DNA structure. To rank the results, Google Scholar applies the same criteria that scientists use when deciding which papers to read, says Acharya, including the importance of the journal and how often the work has been cited. Although you can obtain abstracts for most articles, you or your library will need a subscription to download the full text of some publications. Acharya says upcoming features will include limiting searches by date.
12 November 2004
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When Genes Go Bad
This primer on genetic diseases from the U.S. National Library of Medicine can serve as a reference for students and help teachers catch up on the latest findings. The goal of the Genetics Home Reference is to bridge a gap between researchers and genomics newbies, says project director Alexa McCray: "We were well aware of the wonderful things that have happened as a result of the human genome project, but there was no system that translated that information so that members of the public could understand it."
The handbook section explains topics such as inheritance, different kinds of mutations, genetic testing, and gene therapy. (Above, a virus toting modified DNA slips into a cell.) Users can learn about the genes responsible for illnesses and read up on some 100 conditions, from Alzheimer's disease (certain forms stem from mutations) to X-linked sideroblastic anemia, in which patients make too little hemoglobin. You can browse the descriptions by gene, condition, or chromosome. For readers who want to delve deeper, links lead to technical resources such as PubMed abstracts and gene reviews written for clinicians.
15 October 2004
PhenomicDB is a new tool to help researchers determine how genes contribute to an organism's phenotype, or physical and behavioral characteristics. Compiled by bioinformatics expert Bertram Weiss of the pharmaceutical company Schering AG in Berlin, Germany, and colleagues, the compendium unites information on genes and their effects from WormBase, Online Mendelian Inheritance in Man, FlyBase, and other collections. Data cover humans and model organisms such as yeast, mice, and nematodes, allowing users to search for genes linked to a multitude of phenotypes--from neural tube defects to dwarfism to prostate cancer. By combining far-flung data, PhenomicDB makes it easier to determine which genes trigger similar outcomes in different organisms and to compare the impact of related genes across species.
Proteins and other big molecules look stiff and static on the printed page, but in living cells, their twisting, bending, and flexing help them perform their jobs. Watch the action at the Database of Macromolecular Movements from bioinformatics maven Mark Gerstein of Yale University and colleagues. The site's animations portray the gymnastics of more than 100 proteins and RNA molecules, such as the cytochrome BC1 complex, which plays a key role in oxidative respiration. The flicks can clarify a molecule's function and help drug designers craft more potent compounds. If you have a sample that's not in the database, plug your data into the site's free software to animate its twists and turns.
1 October 2004
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Journey to the Cell's Core
The cell's nucleus is more than just a hangout for DNA. Swarms of proteins congregate there as well, duplicating DNA, bundling it into chromosomes, and performing numerous other jobs. Track down information on these molecules at the
Nuclear Protein Database from the MRC Human Genetics Unit in Edinburgh, U.K. Pick one of the more than 1200 human and mouse proteins found in the nucleus, and you'll discover links to sequence data and PubMed abstracts on its function and location. But the highlight of the site is the backgrounders that describe the proteins housed in different parts of the nucleus. For example, you can peek into the nuclear splicing speckles, which stow proteins that edit newborn RNA strands.
That the nucleus bustles with activity shows through in the dozens of movies you can screen at
Cellnucleus.com, a portal created by Michael Hendzel of the University of Alberta in Edmonton, Canada, and colleague David Pulak. Watch the tiny fibers called microtubules nudging the nucleus around, or catch the chromosomes "decondensing" after cell division. Visitors can also bone up on lab protocols, learn which antibodies work best for visualizing the nuclear goings-on, or study a wealth of tutorials.
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Life Sciences at Your Fingertips
Biology Browser can help you track down information on brown tree snake control in Guam, plan your itinerary for the next big meeting on computers in biology, or find out how air pollution affects flowering times in plants. The life sciences community site and links archive from BIOSIS, a database publisher now owned by Thompson, also links to BIOSIS's zoology teaching resources page.
You can connect to more than 24,000 biology Web sites, from a dictionary of fern terminology to a database of gene-frequency data for different human populations. And the site includes a rundown of hundreds of upcoming conferences as well as links to news stories on fresh research.
17 September 2004
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Parsing RNA
Researchers looking for broad patterns in the sequence or structure of RNA may want to check out Transterm, a tool from the University of Otago in New Zealand. The site lets users analyze RNAs from organisms whose gene sequences are housed in GenBank. For example, visitors can select a species and then determine how often its RNAs use
each of the three-letter codons that designate a specific amino acid. The site also ferrets out motifs: nucleotide sequences or structural quirks that can affect the RNA's stability and how the cell reads it.
30 July 2004
Researchers use reverse transcription PCR to measure amounts of mRNA in a cell and gauge gene activity. Find the right primers for a particular mouse or human gene at this new database from the National Cancer Institute. The site profiles more than 3000 primers and probes, all gleaned from published papers. Search the data by gene, by species, or by assay to find the primer's location, sequence, original reference, and other information.
23 July 2004
The immune system depends on molecules called cytokines to send messages to its defensive cells. To find out more about these proteins and their genes, drop by the Cytokine Family Database from Kumamoto University School of Medicine in Japan. Each search connects you to a wealth of protein and gene databases. For instance, click on the entry for interleukin-6, which prods B cells to divide, and you can compare the gene's sequence across species with Ensembl and learn about its involvement in diseases at Online Mendelian Inheritance in Man. If you want to know more about how cytokines motivate cells, try the linked Cytokine Signaling Pathway Database.
28 May 2004
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Genomics
Grab Bag
If you need help with genome analysis, you might want to take a look at
VISTA, a newly revamped site from the Lawrence Berkeley National
Laboratory in California. Its set of features lets you compare genomes
from the site's collection of nine species or plug in your own
sequences. Try the mVISTA browser to highlight similar and different
regions in, say, a snippet of human DNA compared to that of a chimp's.
Another tool locates attachment sites for transcription factors, which
are proteins that flick genes up and down.
21 May 2004
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Glossing the Genome
Genome Reviews, a new database from the European Bioinformatics Institute (EBI), makes it easier for researchers to track down the latest information on the function of sequenced genes and their proteins. The site adds fresh knowledge to the genome sequences housed in public gene databases by weaving in links to other sites. For example, you can learn more about a protein's function by connecting to the Gene Ontology Annotation database. Locate proteins with similar structural features by jumping to an EBI site called InterPro. So far, Genome Reviews offers upgraded records for more than 150 microbes, and new versions of the database will come online every 2 weeks.
30 April 2004
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Breaking
the Mold
The fungus Aspergillus fumigatus isn't your typically fuzzy,
harmless mold. It picks on patients with AIDS, cystic fibrosis, and
asthma and can incite potentially lethal illness by bedding down in the
lungs, brain, or other organs. Aimed at scientists, doctors, and
patients, The Aspergillus Website from the University of
Manchester, U.K., teems with information about the formidable fungus and
its kin.
Taxonomic accounts describe A. fumigatus and more than 30 other
species. Researchers can browse a database of toxins produced by Aspergillus
varieties or follow lab protocols for tending cultures, testing drug
susceptibility, and other procedures. Scientists haven't quite finished
sequencing the genome of A. fumigatus, but the site offers a
roster of known genes and their functions. Visitors can download slide
shows on the mold's biology and control or watch videos of fungal
filaments growing and tangling with immune cells. Accessing some
sections requires free registration.
9 April 2004
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Fixing Broken Genes
Gene therapy offers the tantalizing promise of curing genetic diseases by repairing the mutations that underlie them. A new federal database, dubbed the Genetic Modification Clinical Research Information System (GeMCRIS), holds protocols for more than 600 gene therapy trials completed or launched since 1990. Users can search the site by disease, investigator, vector, or location, and the database includes abstracts as well as details on methods. Some of the information was already on the Web, but the new collection is "richer" and "easier to navigate," says Allan Shipp of the National Institutes of Health, which developed the site with the U.S. Food and Drug Administration.
GeMCRIS will also allow investigators to submit reports of adverse events during gene therapy trials directly to the database. Although these reports won't be posted on the public part of the Web site, Shipp says this feature will make it easier for agency officials to look across trials for safety problems.
2 April 2004
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Genome Timetable
The mustard plant and the zebrafish are done, the water flea should be finished by the end of the year, and the Jamaican fruit-eating bat is still up in the air. That's the status of projects to sequence these organisms' genomes. This new site from the International Sequencing Consortium tracks the progress of sequencing efforts around the world, listing each project's scheduled or actual completion date and what techniques it is using. Links connect to the group performing the work, the funding sources, and, for completed projects, the final sequence.
26 March 2004
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Coats of Many Colors
Besides plain white, lab mice come in many stylish hues--lethal yellow, black-and-tan, nonagouti sombre, and varitint-waddler, to name a few.
The Coat Colors of Mice, by geneticist Willys Silvers, is a standard reference on the inheritance of this characteristic, which involves more than 50 genes. Published in 1979 but out of print for years, the book is available online at this site from the Jackson Laboratory in Bar Harbor, Maine. Although it predates the mouse genome project, the text is still useful for everyone from animal breeders to students studying gene interactions, to researchers seeking background data about coat color genetics. Links lead to gene sequence info in the lab's Mouse Genome Informatics database.
12 March 2004
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Heads or Tails
The Wnt genes get a developing embryo into shape, helping orchestrate everything from the differentiation of the head and tail ends to the formation of kidney tubules. Faulty
Wnt genes can also spur cancer. Keep tabs on the growing gene family at this site from developmental biologist Roel Nusse of Stanford University.
Tables list all the Wnt genes discovered in model organisms such as Drosophila and in humans--we carry 19. Click on links to gather a gene's DNA and protein sequences or to learn about the proteins it interacts with, which go by names such as Frizzled and Dishevelled. Lab protocols describe techniques such as how to fish out active
Wnt proteins, a feat that Nusse and colleagues first achieved last summer. At right, stimulating a frog embryo to make a
Wnt protein in the wrong place prompts it to sprout a second head.
5 March 2004
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The Many Faces of Immunity
The HLA genes help the immune system discern friend from foe and underlie the rejection of organ transplants. This cadre of genes, which belong to the major histocompatibility complex (MHC), has also drawn interest from anthropologists tracing human migrations and epidemiologists trying to understand the genetic basis of autoimmune diseases. dbMHC, a year-old site from the National Center for Biotechnology Information in Bethesda, Maryland, offers plenty of information for anyone who works with MHC genes and proteins in the lab or the clinic.
MHC genes come in a multitude of forms, or alleles. For example, researchers have identified more than 250 alleles for the HLA-A gene. dbMHC lets you compare different protein versions in 3D and browse the DNA sequences of their genes. The site can also help users select or create typing kits and probes to identify which MHC variants a person carries. A new section lists the frequencies of different MHC alleles in more than 70 populations from places such as Australia, Uganda, and Ireland.
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Cold Spring Harbor Retrospective
Over the years, many of biology's top thinkers have studied, worked, or attended symposia at the Cold Spring Harbor Laboratory on Long Island. In this set of video interviews, more than 50 Cold Spring Harbor alumni--from evolutionist extraordinaire Ernst Mayr of Harvard to science writer Matt Ridley--reminisce about their time at the lab and how it shaped their careers. Aspiring scientists might want to check out the advice from seasoned researchers. For example, Mayr, whose first language was German, hammers home the importance of honing one's writing skills. In another set of interviews on the Human Genome Project, scientists recall their participation in the effort and discuss controversies such as the patenting of human DNA.
13 February 2004
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Biology
Class Gets Wired. A noxious Escherichia coli bacterium nestles onto
a patch of intestinal lining carpeted with microvilli. The image comes
from an animation portraying how the bug coerces an intestinal cell into
building it a comfy resting place.Watch the flick at BioInteractive, an
online teaching trove packed with activities, videos, and other goodies
from the Howard Hughes Medical Institute (HHMI).
6 February 2004
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Genomes United.
Scientists have sequenced the genomes of more than 150 organisms, and they polish off a new one about every week. But comparing these results can be a headache because the data are stashed on multiple Web sites that use different formats and sometimes even different names for the same proteins. Bringing order to this genomic tower of Babel is Cogent, a central storehouse from the European Bioinformatics Institute in Cambridge, U.K. Here, visitors can download a list of predicted proteins for every completed
genome. Moreover, the database's standard nomenclature and organization makes it easier to contrast different species.
2 June 2000
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Munching on Strange
Chemicals. Microbes that devour or otherwise help break down exotic
chemicals are cleaning up the environment, spawning new technologies,
and deepening our understanding of microbial life. While biodegradation
and biocatalysis are young fields, much of what is known can be found in
the University of Minnesota Biocatalysis/Biodegradation Database.
The site provides detailed explanations of 99 "pathways"
chains of reactions that break down various chemicals as well as data on
hundreds of individual reactions, compounds, enzymes, and
microorganisms. The site focuses on the reactions that begin to break
down compounds not commonly found in nature, for example, those
involving naphthalene, the stuff of mothballs. For information on the
more common metabolic pathways that complete the breakdown, the site
links to databases such as the
Kyoto Encyclopedia of Genes and Genomes . All data display their
pedigrees, and a guided tour helps first time visitors find their way
around.
19 May 2000
12 May 2000
14 April 2000
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Model T. Need
to help finding major sites for mouse or Xenopus. The
National Institutes of Health hub is a handy launch pad to genome
databases and other links for eight model organisms :mouse, rat, S. cerevisiae (budding yeast),
D. discoideum (social amoebae), C. elegans (round worm), D. melanogaster (fruit fly),
D. rerio (zebrafish) and Xenopus (frog).
7 April 2000
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Net lore. Wondering who
invented Usenet, or what exactly is an Internet Relay Chat? This site
explains the nuts and bolts of the Net and serves up profiles of those
who shaped it, such as Vannevar Bush, whose 1945 article on "memex,"
a device for storing information, presaged the Web.
17 March 2000
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Molecular profiles.
Putting a
face on the 10,000 structures in the Protein Data Bank is a new feature
called Molecule of the Month, brief articles written by a scientist that
describe the biology and role in society of all important molecules.
Coming in April: the most common protein in the human body.
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