You are currently browsing the archives for the Interesting Studies category.

Archive for the ‘Interesting Studies’ Category

Cancer Leaves a Common Fingerprint on DNA

 :: Posted by American Biotechnologist on 08-26-2014

Regardless of their stage or type, cancers appear to share a telltale signature of widespread changes to the so-called epigenome, according to a team of researchers. In a study published online in Genome Medicine on Aug. 26, the investigators say they have found widespread and distinctive changes in a broad variety of cancers to chemical marks known as methyl groups attached to DNA, which help govern whether genes are turned “on” or “off,” and ultimately how the cell behaves. Such reversible chemical marks on DNA are known as epigenetic, and together they make up the epigenome.

“Regardless of the type of solid tumor, the pattern of methylation is much different on the genomes of cancerous cells than in healthy cells,” says Andrew Feinberg, M.D., M.P.H., a professor of medicine, molecular biology and genetics, oncology, and biostatistics at the Johns Hopkins University School of Medicine. Feinberg led the new study along with Rafael Irizarry, Ph.D., a professor of biostatics at Harvard University and the Dana-Farber Cancer Institute. “These changes happen very early in tumor formation, and we think they enable tumor cells to adapt to changes in their environment and thrive by quickly turning their genes on or off,” Feinberg says.

Feinberg, along with Johns Hopkins University School of Medicine oncology professor Bert Vogelstein, M.D., first identified abnormal methylation in some cancers in 1983. Since then, Feinberg’s and other research groups have found other cancer-associated changes in epigenetic marks. But only recently, says Feinberg, did researchers gain the tools needed to find out just how widespread these changes are.

For their study, the research team took DNA samples from breast, colon, lung, thyroid and pancreas tumors, and from healthy tissue, and analyzed methylation patterns on the DNA. “All of the tumors had big blocks of DNA where the methylation was randomized in cancer, leading to loss of methylation over big chunks and gain of methylation in smaller regions,” says Winston Timp, Ph.D., an assistant professor of biomedical engineering at Johns Hopkins. “The changes arise early in cancer development, suggesting that they could conspire with genetic mutations to aid cancer development,” he says.

The overall effect, Feinberg says, appears to be that cancers can easily turn genes “on” or “off” as needed. For example, they often switch off genes that cause dangerous cells to self-destruct while switching on genes that are normally only used very early in development and that enable cancers to spread and invade healthy tissue. “They have a toolbox that their healthy neighbors lack, and that gives them a competitive advantage,” Feinberg says.

“These insights into the cancer epigenome could provide a foundation for development of early screening or preventive treatment for cancer,” Timp says, suggesting that the distinctive methylation “fingerprint” could potentially be used to tell early-stage cancers apart from other, harmless growths. Even better, he says, would be to find a way to prevent the transition to a cancerous fingerprint from happening at all.

Thanks to Johns Hopkins Medicine for contributing this story.

Single gene controls jet lag

 :: Posted by American Biotechnologist on 08-13-2014

Scientists at the Salk Institute for Biological Studies have identified a gene that regulates sleep and wake rhythms.

The discovery of the role of this gene, called Lhx1, provides scientists with a potential therapeutic target to help night-shift workers or jet lagged travelers adjust to time differences more quickly. The results, published in eLife, can point to treatment strategies for sleep problems caused by a variety of disorders.

“It’s possible that the severity of many dementias comes from sleep disturbances,” says Satchidananda Panda, a Salk associate professor who led the research team. “If we can restore normal sleep, we can address half of the problem.”

Read more…

A Revolution in Scientific Publication

 :: Posted by American Biotechnologist on 07-30-2014

Since we are talking about impact factors and Journal related stuff, (see When JIF Becomes a Dirty Word), I wanted to share with you a very cool concept that I saw recently in F1000 Research.

Aside from it’s move to the digital world, scientific publication, as we know it, has remained relatively constant for over four hundred years. Papers are written in a scientific method-based theme and broken down into bite size sections. Papers are very much there for scientists to communicate their findings with us and for the investigators to provide us with their personal interpretation of the data. While a sort of 2-way communication often happens via editorials and personal communication, the presentation of the data remains static and one dimensional. Results, which represent the heart of the researchar, often presented in tabular or pictorial format. Much of the effort and funding allocated to a research project can be distilled down to several figures and maximizing the communicative ability of these results is essential to successful publication. That is why the methodology used to publish a recent paper in the journal F1000 Research may, in fact, revolutionize the world of scientific publishing.

In the newly released article, German professor of neurogenetics, Bjorn Brembs, published a proof-of-concept figure allowing readers and reviewers to run the underlying code within the online article. Instead of presenting readers with a static figure that can only be interpreted by the author, Dr. Brembs submitted the figure’s underlying code to the journal, allowing readers and reviewers to render the figure in various formats giving them more control over interpretation of the original data.

According to Brembs, the ultimate goal is to set up all journal submissions in such a way that authors will no longer have to deal with figures. They will simply need to submit text with links to data and code, and the rest will be up to the reader.

The recent rise in retraction rates of scientific articles proves that attempts at reproducibility by other labs are crucial to cross-checking our understanding of science. With only one or two figures to choose from in the past, authors were incentivized to pick the view of the data that best demonstrated their conclusions. “The traditional method of publishing still used by most journals today means that as a referee or reader, the data cannot be reused nor can the analysis be checked to see if all agree with the reported conclusions”, said Brembs. “This slows down scientific discovery. We are pleased to be able to pioneer these two interactive figures with F1000Research, which will hopefully be the start of a big shift in the way journals treat their figures.”

Viruses May Not Be So Bad After All

 :: Posted by American Biotechnologist on 07-22-2014

In contrast to their negative reputation as disease causing agents, some viruses can perform crucial biological and evolutionary functions that help to shape the world we live in today, according to a new report by the American Academy of Microbiology.

“Viruses participate in essential Earth processes and influence all life forms on the planet, from contributing to biogeochemical cycles, shaping the atmospheric composition, and driving major speciation events,” states Marilyn Roossinck of Pennsylvania State University, a member of the steering committee that helped to organize the colloquium.

The report, ‘Viruses Throughout Life & Time: Friends, Foes, Change Agents,’ is based on the deliberation of a group of scientific experts who gathered for two days in San Francisco, CA in July 2013 to answer a series of questions regarding the variety of roles that viruses play in the natural world.

“The inspiration for holding the colloquium was that recent metagenomics studies of viruses have indicated we know very little about the real world of viruses. Almost all published research is about the viruses that cause disease in humans and their domesticated plants and animals. This certainly represents only a very small fraction of the viruses that really exist,” says Roossinck. “It is very important to understand the real world of viruses, as this can inform our basic understanding of life and its origins, as well as major earth phenomena like carbon cycling.”

Beyond their pathogenic impact, the report examines in depth the size of the virosphere, the origin of viruses, the overlooked biological and microbial ecological role of viruses, and how these live forms have contributed to evolution. Additional highlights from the report explain how some viruses are commensal organisms or symbionts, their functioning in microbial communities, and their role in maintaining the biosphere. The array of responsibilities taken on by viruses is due to their incredible sequence diversity and genomic plasticity, referred to as “viral dark matter”.

The report concludes by stimulating the readers to think about key questions: “What if viruses had never existed on Earth? Would life have evolved quite differently”? Continued viral research will help to answer these enticing questions.

Thank you to the American Society of Microbiology for contributing this story.

Turning Stem Cells into Blood

 :: Posted by American Biotechnologist on 07-14-2014

The ability to reliably and safely make in the laboratory all of the different types of cells in human blood is one key step closer to reality.

Writing today in the journal Nature Communications, a group led by University of Wisconsin-Madison stem cell researcher Igor Slukvin reports the discovery of two genetic programs responsible for taking blank-slate stem cells and turning them into both red and the array of white cells that make up human blood.

The research is important because it identifies how nature itself makes blood products at the earliest stages of development. The discovery gives scientists the tools to make the cells themselves, investigate how blood cells develop and produce clinically relevant blood products.

“This is the first demonstration of the production of different kinds of cells from human pluripotent stem cells using transcription factors,” explains Slukvin, referencing the proteins that bind to DNA and control the flow of genetic information, which ultimately determines the developmental fate of undifferentiated stem cells.

During development, blood cells emerge in the aorta, a major blood vessel in the embryo. There, blood cells, including hematopoietic stem cells, are generated by budding from a unique population of what scientists call hemogenic endothelial cells. The new report identifies two distinct groups of transcription factors that can directly convert human stem cells into the hemogenic endothelial cells, which subsequently develop into various types of blood cells.

The factors identified by Slukvin’s group were capable of making the range of human blood cells, including white blood cells, red blood cells and megakaryocytes, commonly used blood products.

Read more…