Sam Jaffe
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Articles by Sam Jaffe

Iron Seeding Just Doesn't Pay
Sam Jaffe | | 6 min read
BRINGING ON THE NEXT ICE AGE?Dee Breger, Drexel UniversityAssumptions that tiny diatoms such as the ones shown above could fix carbon from the air and sink it to the bottom of the ocean have been hard to prove.The US Department of Energy has taken an interest in carbon sequestration, but a grand scheme to induce thick blooms of carbon-fixing algae has yet to bear fruit in early studies. The DOE directs a large share of its global warming budget to carbon-sequestration research, drawing on biolog

Systems Biology on the Grid
Sam Jaffe | | 1 min read
Courtesy of CellwareThere are more than 60 in silico modeling programs available to systems biologists, including expensive proprietary packages and niche open-source projects. Most of them, though, rely on one kind of algorithm to calculate a model.That's why Pawan Kumar Dhar, a senior research scientist at the Bioinformatics Institute in Singapore, designed Cellware http://www.bii.a-star.edu.sg/research/sbg/cellware/index.asp. "In gene expression, you would usually use deterministic algorithms

Recycling the Energy of Waste
Sam Jaffe | | 1 min read
Every resource carried onto a manned spaceship is precious, because it costs hundreds of dollars to lift each pound of material past Earth's surly bonds. Now that NASA is in the process of planning a trip to Mars that might take up to two years, no type of recycling can be overlooked. One thing that can provide three basic raw materials (water, energy, and fertilizer) needed for a long space journey: human waste.Most methods of recycling organic waste involve the production of methane, a flammab

A Bioassay with a Heart of Gold
Sam Jaffe | | 3 min read
EXQUISITE SENSITIVITY:In the new assay system used at the Mirkin lab, the protein to be detected (in this case, prostate specific antigen, PSA) is sandwiched between a magnetic microparticle (MMP) and a gold nanoparticle (NP). The system detects the bio-bar-codes present on the NPs with sensitivity five orders of magnitude greater than that of ELISA. (Reprinted with permission, Science, 301:1884–6, 2003.)As any 5-year-old child will tell you, magnets are great for lifting things off the fl

The Basics of Biotechnology
Sam Jaffe | | 2 min read
What does 'bio-technology' mean?The term comes from Fernando Silva da Bioteqnolojo, a 16th century venture capitalist who sold shares in the Fountain of Youth to Madrid laborers. Not buying it? Okay, biotechnology is a term that first appeared in the 1970s to describe the use of biological techniques for creating commercially useful products, mostly protein-based pharmaceuticals. One of the first successful biotech companies, Genentech, found a way to produce insulin using vats filled with anaer

Humanizing Protein Splicing
Sam Jaffe | | 5 min read
IT SLICES, IT DICES, IT EVEN SPLICES:©2004 Nature Publishing Group H.-G. Rammensee, Nature, 427:203–4, Jan. 15, 2004.Initial models of protein splicing (as shown at left) had protein cleavage and ligation occurring through unidentified processes, with further truncation occurring in the proteasome. Further evidence suggests that the proteasome actually mediates both hydrolysis and reformation of amide bonds (as shown at right) and that remaining N-terminal amino acids are removed in t

An Early Look at a Killer
Sam Jaffe | | 1 min read
Reprinted from T.D. Brock, Robert Koch: A Life in Medicine and Bacteriology, Science Tech Publishers: Madison, WI, 1988, pg. 51, Fig 6.5Robert Koch (1843–1910) was a country doctor from the German hinterlands of what is now Poland. He liked to investigate samples from his barnyard animals under a microscope. He went on to become the world's first and one of its greatest bacteriologists, winning the Nobel Prize in 1905. Although famed for his work on tuberculosis and the postulates named af

Gel Annotation on a Budget
Sam Jaffe | | 1 min read
Proteomicists who want to share their data, take heed: A team at the University of Alberta has a software tool for you. GelScape http://www.gelscape.ualberta.ca is a free, cross-platform, browser-based tool for annotating, manipulating, comparing, and storing 1-D and 2-D protein images.1 Users can run the Java-based software off servers in Edmonton or install a local copy on their individual PC, according to David Wishart, a bioinformatics professor at the University of Alberta who oversaw the p

Facing the Global Water Crisis
Sam Jaffe | | 10+ min read
DRY EARTH:Photo by Roger Lemoyne/LiaisonA woman sits on the ancient steps that once led down to Lake Rajsamand near Udaipur, India. The lake dried up in 2000 due to drainage of its feeder rivers for agricultural purposes and drought.Eli Raz, an Israeli geologist, found himself in something of a hole, and a rather deep one. He had stopped his car on a desert highway near his home by the Dead Sea to inspect some rock formations. As he was walking a few hundred meters from the road, he felt a rumbl

Taking Control of the Cluster
Sam Jaffe | | 1 min read
When Gernot Stocker noticed that the biologists in his lab were not using the department's brand-new, 24-node computer cluster, he started taking notes. Running sequences on a desktop computer could take days, yet these scientists preferred that to the cluster for a simple reason. "Biologists don't like command-line software," says Stocker, a graduate student at the Institute for Genomics and Bioinformatics at Graz University of Technology in Austria. "They're used to using Web browsers."So Stoc

Clinicians sentenced to death
Sam Jaffe | | 2 min read
Foreigners worked in a Libyan hospital where 426 children were infected with HIV

The Day the Earth Stood Still
Sam Jaffe | | 1 min read
Courtesy of Harry Ransom Center, U of Texas at AustinThere are many milestones on the road to modern science, but few equal the summer afternoon in 1826 when French inventor Joseph Nicephore Niepce (1765–1833) captured the first permanent image. Niepce, a tinkerer and amateur scientist, set out to automate the lithography process in 1812. Experiments with various acids and other substances failed. Still tinkering 15 years later, he set up a pewter plate layered with photosensitive bitumen












