Category Archives: Education

Geothite

Photo of Geothite, FeO(OH), Hydrated Iron Oxide, at the Smithsonian Natural History Museum in Washington DC, by John Hunter. Related:Science and Engineering Web Search – Boston Science Museum photos

DNA Seen Through the Eyes of a Coder

Great paper looking at DNA from the perspective of a computer programmer. DNA seen through the eyes of a coder by Bert Hubert:

The language of DNA is digital, but not binary. Where binary encoding has 0 and 1 to work with (2 – hence the ‘bi’nary), DNA has 4 positions, T, C, G and A. Whereas a digital byte is mostly 8 binary digits, a DNA ‘byte’ (called a ‘codon’) has three digits. Because each digit can have 4 values instead of 2, an DNA codon has 64 possible values, compared to a binary byte which has 256.

A typical example of a DNA codon is ‘GCC’, which encodes the amino acid Alanine. A larger number of these amino acids combined are called a ‘polypeptide’ or ‘protein’, and these are chemically active in making a living being.
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Furthermore, 97% of your DNA is commented out. DNA is linear and read from start to end. The parts that should not be decoded are marked very clearly, much like C comments. The 3% that is used directly form the so called ‘exons’. The comments, that come ‘inbetween’ are called ‘introns’.

Young Geneticists Making a Difference

After an early phase of discouragement, Johannes Krause was able to follow his long interest in genetics and even link it to another passion of his, paleoanthropology. Krause initially chose to study biochemistry at the University of Leipzig. But “I was almost about to quit” at the frustration of learning much more about basic chemistry than biology, he says. However, in the third year of his bachelor’s degree, he took some specialised courses in genetics as an Erasmus student at the University College Cork in Ireland that revived his interest for the field.

Back in Leipzig, a summer internship on comparing gene expression between humans and chimpanzees at the Max Planck Institute for Evolutionary Anthropology sparked Krause’s enthusiasm for good. He stayed on in the lab as a research assistant for 2 years before graduating in 2005. While there, Krause helped develop a biological method to read large pieces of ancient DNA, sequence the complete mitochondrial genome of the mammoth from fossil samples, and place it in the context of evolution. “Johannes has great technical skill and the judgment to distinguish a good project from a blind alley. Like few others he can see the interesting pattern that can hide in sometimes confusing data,” Svante PÃ¤Ã¤bo, his principal investigator, writes in an e-mail to Science Careers.

Cu₂C0₃(OH)₂

Photo of Malachite, Cu₂C0₃(OH)₂, copper(II) carbonate hydroxide, at the Smithsonian Natural History Museum in Washington DC, by John Hunter. Related: United States Botanical Garden photos – Science and Engineering Web Search

New Drug Targets May Fight Tuberculosis in Novel Way

New Drug Targets May Fight Tuberculosis and Other Bacterial Infections in Novel Way

“We have developed the first inhibitor of a key small molecule from Mycobacterium tuberculosis and Mycobacterium leprae (which causes leprosy) utilized to subvert human host’s defenses and damage and invade human host’s cells during infection,” explains study senior author Dr. Luis Quadri, Associate Professor of Microbiology and Immunology at Weill Cornell.
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“We are moving beyond antimicrobials such as antibiotics, which kill the bacterium directly, to anti-infectives, that may have no effect against the pathogen in the test tube but which do compromise its ability to infect and spread in the host,” he explains. “We believe that the expansion of the drug armamentarium to include such anti-infective drugs could help the fight against multi-drug resistant infection that has become such a challenge today.”
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“I believe that drugs targeting virulence factors are just one component of the paradigm shift in the antimicrobial drug discovery for the 21st century—one that will offer patients more options in the fight against truly global killers,” he says.

LEGO Project Inspires Students

LEGO project inspires students

After school every Thursday at New Haven Elementary more than 60 students gather to discuss energy sources, plan building models, and learn more about science and engineering. The group, made up of first-, second- and third-graders, is participating in Junior First LEGO League (JFLL). JFLL is a worldwide organization that introduces children to concepts of teamwork and basic design skills.

Karen Cheser, elementary director of teaching and learning for Boone County Schools, brought the program to the district. It relies on 10 volunteer coaches including school teachers, a robotics engineer, parents, and business owners to guide students.
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“Participation is very active because of the hands-on component of the work,” Fortner said. “Students see it as a club, but we look at it as an extension of the school day, because it teaches fundamental science concepts, it encourages teamwork, and builds social skills.”

The First Lego League web site provides information on local programs all over the world.

Molecular Bioengineering and Dynamical Models of Cells

Study Maps Life in Extreme Environments, Creating Potential for Molecular Bioengineering and Dynamical Models of Cells

The researchers focused on a little studied organism that can survive high salt, radiation, and other stresses that would be deadly to most other organisms. By focusing on such an organism the researchers were able to show definitively that they could understand and model the circuit controlling the cell directly from experiments designed to measure all genes in the genome simultaneously. These are called systems-biology experiments. This scholarship is part of a new scientific field, systems biology, which examines how genes influence each other via extremely large networks of interaction and how these networks respond to stimuli, adapting over time to new environments and cell states.
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“This is also a good model to explain how, in general, cells make stable decisions as they move through time scales,” added Bonneau, who is part of an NYU research group that handled the analysis of this genome. “If you want to understand how cells respond to their environments, the model offers a clearer window than previously existed for this domain of life.” The collaboration between Baliga’s and Bonneau’s research groups represents a type of partnership becoming more essential to biological and biomedical research: biologists and computer scientists teaming up to design experiments and analysis that synergize to decipher living systems, resulting in ever more complex and accurate models of the cell.

Science Explained: Genetics

The latest 1 page summary of a science topic from Seed Magazine – Genetics cribsheet:

The field of genetics deals with the way living things store and use information required for their development and behavior. This Cribsheet covers the basics of molecular genetics: DNA replication, the genetic code, and gene expression. In addition, we tell you how genome sequencing has progressed over the last decade and what researchers hope to accomplish with synthetic biology.

Smart Squirrels Sneaky Snake Strategy

Squirrels Use “Snake Perfume” to Fool Predators

To mask their odor from rattlesnakes, California ground squirrels and rock squirrels chew on sloughed-off snake skin and smear it on their fur, according to a new study. The act most likely persuades the predators that another snake, not a squirrel, is in the area.

“To our knowledge this is the first case where [this idea] has been tested systematically and shown to have an anti-predator function—protecting the squirrel from rattlesnake predation,” said study lead author Barbara Clucas.Rattlers and other snakes usually prey on baby squirrels, because the adults have proteins in their blood that make them immune to snake venom.

Pups, on the other hand, aren’t big enough to resist the poison. Clucas and colleagues therefore think that adult female and juvenile squirrels spend more time applying snake scent to their bodies. “Adult females actively protect their pups … and share their burrows with juveniles,” Clucas said.

Africa Turning to China and India for Engineering and Science Education

‘Browning’ the technology of Africa by G. Pascal Zachary

The sudden influx of Chinese and Indian technologies represents the “browning” of African technology, which has long been the domain of “white” Americans and Europeans who want to apply their saving hand to African problems.

“It is a tectonic shift to the East with shattering implications,” says Calestous Juma, a Kenyan professor at Harvard University who advises the African Union on technology policy. One big change is in education. There are roughly 2,000 African students in China, most of whom are pursuing engineering and science courses. According to Juma, that number is expected to double over the next two years, making China “Africa’s leading destination for science and engineering education.”

China’s technology inroads are usually less dramatic, but no less telling. In African medicine, Chinese herbs and pharmaceuticals are quietly gaining share. For example, the Chinese-made anti-malarial drug artesunate has become part of the standard treatment within just a few years. Likewise, Chinese mastery over ultra-small, cheap “micro-hydro” dams, which can generate tiny amounts of electricity from mere trickles of water, appeals to power-short, river-rich Africans. Tens of thousands of micro-hydro systems operate in China, and nearly none in Africa.