Category Archives: Life Science

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.

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.

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.

Brain Development

Making the Mind, Why we’ve misunderstood the nature-nuture debate by Gary Marcus

The mapping between genes and behavior is made even more complex by the fact that few if any neural circuits operate entirely autonomously. Except perhaps in the case of reflexes, most behaviors are the product of multiple interacting systems. In a complex animal like a mammal or a bird, virtually every action depends on a coming together of systems for perception, attention, motivation, and so forth. Whether or not a pigeon pecks a lever to get a pellet depends on whether it is hungry, whether it is tired, whether there is anything else more interesting around, and so forth. Furthermore, even within a single system, genes rarely participate directly “on-line,” in part because they are just too slow. Genes do seem to play an active, major role in “off-line” processing, such as consolidation of long-term memory—which can even happen during sleep—but when it comes to rapid on-line decision-making, genes, which work on a time scale of seconds or minutes, turn over the reins to neurons, which act on a scale of hundredths of a second. The chief contribution of genes comes in advance, in laying down and adjusting neural circuitry, not in the moment-by-moment running of the nervous system. Genes build neural structures—not behavior.

An interesting read on brain development. This is another topic I find very interesting.

Science Explained: What The Heck is a Virus?

What The Heck is a Virus? [removed broken link]

A virus is not strictly alive.. nor is it strictly dead… A virus has some fundamental information (genes made of DNA or RNA) which allows it to make copies of itself. However, the virus must be inside a living cell of some kind before the information can be used. In fact, the information won’t be made available unless the virus enters a living cell. It is this entrance of a virus into a cell which is called a viral infection. Too, the virus is very, very small relative to the size of a living cell. Therefore, the information the virus can carry is actually not enough to allow it to make copies (replicate). The virus uses the cell’s machinery and some of the cell’s enzymes to generate virus parts which are later assembled into thousands of new, mature, infectious virus which can leave the cell to infect other cells.

Giant Rats

Giant rat found in ‘lost world

The trip was the second time that CI had visited the Foja Mountains, part of the Mamberamo Basin, the largest pristine tropical forest in the Asia Pacific region. In 2005, the area was dubbed a “lost world” after scientists discovered dozens of new plants and animals in the dense jungle.
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the most surprising finds of the trip were the two new species of mammal – the Cercarteus pygmy possum and Mallomys giant rat. “The giant rat is about five times the size of a typical city rat,” said Kristofer Helgen, a scientist with the Smithsonian Institution in Washington, D.C. “With no fear of humans, it apparently came into the camp several times during the trip.”

Handcrafted Chromosomes

Synthetic DNA on the Brink of Yielding New Life Forms

Scientists in Maryland have already built the world’s first entirely handcrafted chromosome — a large looping strand of DNA made from scratch in a laboratory, containing all the instructions a microbe needs to live and reproduce.

In the coming year, they hope to transplant it into a cell, where it is expected to “boot itself up,” like software downloaded from the Internet, and cajole the waiting cell to do its bidding. And while the first synthetic chromosome is a plagiarized version of a natural one, others that code for life forms that have never existed before are already under construction.
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LS9 Inc., a company in San Carlos, Calif., is already using E. coli bacteria that have been reprogrammed with synthetic DNA to produce a fuel alternative from a diet of corn syrup and sugar cane. So efficient are the bugs’ synthetic metabolisms that LS9 predicts it will be able to sell the fuel for just $1.25 a gallon.

At a DuPont plant in Tennessee, other semi-synthetic bacteria are living on cornstarch and making the chemical 1,3 propanediol, or PDO. Millions of pounds of the stuff are being spun and woven into high-tech fabrics (DuPont’s chief executive wears a pinstripe suit made of it), putting the bug-begotten chemical on track to become the first $1 billion biotech product that is not a pharmaceutical.

Engineers at DuPont studied blueprints of E. coli’s metabolism and used synthetic DNA to help the bacteria make PDO far more efficiently than could have been done with ordinary genetic engineering.

Related: Life-patents – Open-Source Biotech

Another Bacteria DNA Trick

A DNA shift never before seen in nature

For several decades, researchers have known that it is possible to modify synthetic oligonucleotides (short strands of DNA) by adding sulfur to the sugar-phosphate DNA backbone as a phosphorothioate. Researchers often use such modifications in the laboratory to make DNA resistant to nucleases (enzymes that snip DNA in certain locations) as a step toward gene and antisense therapies of human diseases.

Dedon said he and his co-workers were surprised to discover that a group of bacterial genes, known as the dnd gene cluster, gives bacteria the ability to employ the same modification on their own. “It turns out that nature has been using phosphorothioate modifications of DNA all along, and we just didn’t know about it,” he said.
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He theorizes that the modification system might serve as either protection against foreign (unmodified) DNA, or as a “bookmark” to assist with transcription or replication of DNA.

Bacteria really are amazing. I am starting to read more about bacteria and virus so maybe I will post more on these topics over the next few months.

Orcas Create Wave to Push Seal Off Ice

Pretty amazing footage. From Nature News, Unique orca hunting technique documented:

Ingrid Visser of the Orca Research Trust in New Zealand and her colleagues report on six further observations of the animals using group hunting behaviour to divide ice floes, push them into open water, and create waves to wash animals off them into their waiting jaws.