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Archive for the ‘Interesting Studies’ Category

How Statistics Can Help Minimize Scientific Retractions

 :: Posted by American Biotechnologist on 03-03-2014

The ability to duplicate an experiment and its results is a central tenet of the scientific method, but recent research has shown an alarming number of peer-reviewed papers are irreproducible.

A team of math and statistics professors has proposed a way to address one root of that problem by teaching reproducibility to aspiring scientists, using software that makes the concept feel logical rather than cumbersome.

Researchers from Smith College, Duke University and Amherst College looked at how introductory statistics students responded to a curriculum modified to stress reproducibility. Their work is detailed in a paper published Feb. 25 in the journal Technological Innovations in Statistics Education.

In 2013, on the heels of several retraction scandals and studies showing reproducibility rates as low as 10 percent for peer-reviewed articles, the prominent scientific journal Nature dedicated a special issue to the concerns over irreproducibility.

Nature’s editors announced measures to address the problem in its own pages, and encouraged the science community and funders to direct their attention to better training of young scientists.

“Too few biologists receive adequate training in statistics and other quantitative aspects of their subject,” the editors wrote. “Mentoring of young scientists on matters of rigour and transparency is inconsistent at best.”

The authors of the present study thus looked to their own classrooms for ways to incorporate the idea of reproducibility.

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3D Printer Used to Print Vascularized Human Tissue

 :: Posted by American Biotechnologist on 02-27-2014

The Wyss Institute at Harvard University is using engineering principles to build living things, and create biologically inspired materials and devices. In this really cool video, scientists use a custom built 3D printer to print vascularized tissue which will eventually be used as replacements for damaged human tissue.

To read more about this story see An Essential Step toward Printing Living Tissues.

A Genetic Explanation of Why You May Look More Like Your Mother

 :: Posted by American Biotechnologist on 02-24-2014

We are a product of our parents. Maybe you have your mother’s large, dark eyes, and you inherited your father’s infectious smile. Both parents contribute one copy, or allele, of each gene to their offspring, so that we have two copies of every gene for a given trait – one from mom, the other from dad. In general, both copies of a gene are switched on or off as an embryo develops into an adult. The “switching on” of a gene begins the process of gene expression that ultimately results in the production of a protein.

Occasionally, a cell will arbitrarily begin to use of one copy of a gene over the other. The activation of only one member of a gene pair is called ”monoallelic gene expression.” In work published today in Developmental Cell, a team of researchers led by Professor David Spector at Cold Spring Harbor Laboratory (CSHL) shows that this random phenomenon is far more likely to be found in mature, developed cell types than in their stem cell precursors. This, in turn, offers an unexpected glimpse of randomness and variability in gene expression.

Cells are exquisitely sensitive to protein amounts: too much or too little can give rise to diseases, including cancer. For example, certain proteins, called tumor suppressors, act as “stop” signals to restrain cell growth. A cell with only half the dosage of such a protein may become the seed of a tumor. Random monoallelic gene expression cuts the amount of a protein by half, suggesting that this type of variability may have significant implications for disease.

Spector and Mélanie Eckersley-Maslin, Ph.D., lead author on the new paper, found that monoallelic gene expression is truly a random process. “It is not deterministic in any way,” says Spector. “This significant amount of flexibility and randomness in gene expression is important for adaptation as a species evolves, but it is unclear how it functions in organisms today.”

To better understand when monoallelic gene expression is established, Spector and his team collaborated with researchers from the European Molecular Biology Laboratory. The team used advanced sequencing technology and analysis tools to globally assess allele usage in two different cell types. They compared embryonic stem cells, which can change, or “differentiate,” into nearly any type of tissue, with cells that had already differentiated into the precursors of neurons. They found a 5.6-fold increase in the number of monoallelically expressed genes in the differentiated cells. “As differentiation occurs, there is a dramatic change in gene expression as a specific program or set of genes is selected to be expressed and a massive reorganization occurs in the nucleus,” says Spector. “It is these enormous changes that lead to stochastic (i.e., variable) monoallelic expression.”

The team was surprised to find that 8% of the monoallelically expressed genes were able to boost their level of expression to compensate for what would otherwise be a shortfall. The researchers speculate that the cell may require higher amounts of protein from those genes. “This work raises many important questions,” says Spector, “such as: how does the cell know how much of each protein to produce? How much flexibility is there? What is the tipping point toward disease?” The team continues to explore these fascinating questions.

This work was supported by the National Institute of General Medical Sciences and the National Cancer Institute, a Genentech Foundation Fellowship, George A. and Marjorie H. Anderson Fellowship, Deutscher Akademischer Austauschdienst Postdoctoral Fellowship, the European Molecular Biology Laboratory, and the Wellcome Trust.

“Random Monoallelic Gene Expression Increases upon Embryonic Stem Cell Differentiation” appears online in Developmental Cell on February 24, 2014. The authors are: Mélanie A. Eckersley-Maslin, David Thybert, Jan H. Bergmann, John C. Marioni, Paul Flicek, and David L. Spector. The paper can be obtained online at:

Thanks to Cold Spring Harbor Laboratory for contributing this story.

Pied Piper Approach to Killing Cancer

 :: Posted by American Biotechnologist on 02-17-2014

One factor that makes glioblastoma cancers so difficult to treat is that malignant cells from the tumors spread throughout the brain by following nerve fibers and blood vessels to invade new locations. Now, researchers have learned to hijack this migratory mechanism, turning it against the cancer by using a film of nanofibers thinner than human hair to lure tumor cells away.

Instead of invading new areas, the migrating cells latch onto the specially-designed nanofibers and follow them to a location – potentially outside the brain – where they can be captured and killed. Using this technique, researchers can partially move tumors from inoperable locations to more accessible ones. Though it won’t eliminate the cancer, the new technique reduced the size of brain tumors in animal models, suggesting that this form of brain cancer might one day be treated more like a chronic disease.

“We have designed a polymer thin film nanofiber that mimics the structure of nerves and blood vessels that brain tumor cells normally use to invade other parts of the brain,” explained Ravi Bellamkonda, lead investigator and chair of the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University. “The cancer cells normally latch onto these natural structures and ride them like a monorail to other parts of the brain. By providing an attractive alternative fiber, we can efficiently move the tumors along a different path to a destination that we choose.”

Details of the technique were reported February 16 in the journal Nature Materials. The research was supported by the National Cancer Institute (NCI), part of the National Institutes of Health; by Atlanta-based Ian’s Friends Foundation, and by the Georgia Research Alliance. In addition to the Coulter Department of Biomedical Engineering, the research team included Children’s Healthcare of Atlanta and Emory University.

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Bilingual Bacteria

 :: Posted by American Biotechnologist on 01-28-2014