Getting DNA or RNA into cells can be a tricky business, and a variety of transfection reagents have been developed over the years to make the process easier. Lipid-based reagents are especially popular because they combine efficient transfection with relatively low toxicity.
Yesterday, a series of 27 papers representing the most comprehensive genomic analysis of human cancers to date was published in Cell Press journals.
The collection constitutes the final outputs from the Cancer Genome Atlas (TCGA) project, a collaboration between the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI) involving analysis of over 11,000 tumors representing 33 different cancers. The many research teams involved analyzed tumor DNA, mRNA, miRNA and chromatin, comparing them to matched normal cellular genomes to perform a complete molecular characterization of cancer-specific changes. The results have been presented with much hope that open access to this type of comprehensive analysis will build on recent advances in understanding tumor biology and spur further progress in developing new approaches to treatment. (See this news item for more detail).
The Pan-Cancer Atlas results are collected on a cell.com portal, where they are presented in three collections grouped by topic: Cell of Origin, Oncogenic Processes and Signaling Pathways. Each collection is accompanied by a “Flagship” paper introducing the topic and summarizing the findings. It seems fitting that these findings have been published in #HumanGenomeMonth. This comprehensive analysis of the genomic and metagenomic profiles of tumors illustrates one powerful application of the type of genomic analysis pioneered by the original Human Genome Project, and shows just how much has been made possible since the initial publication of the human genome fifteen years ago. Continue reading “The Pan-Cancer Atlas: “The End of the Beginning””
Several weeks ago, I came across an article on ScienceNews.org about how Wikipedia is becoming a scientific resource, whether we like it or not. Scientists are reading Wikipedia, the article said, and it’s affecting how they write. The article cited a study by researchers from MIT and Pitt that found statistical evidence of language in peer-reviewed articles being influenced by Wikipedia articles relevant to the topic. They concluded that journal articles referenced in Wikipedia are subsequently cited more than other similar articles, and that on a semantic level, Wikipedia is influencing the language of scientific journal articles at an astounding rate.
I was intrigued by the idea that reading Wikipedia affects how we later write about a subject. When I start writing about a new topic, the first thing I do is head to Wikipedia to gather a basic understanding before I dive into journal articles. I’ll skim through the overview and most relevant subsections, then check out the references to see what I should continue reading. However, the findings of the study imply that even though I don’t directly use information or language from Wikipedia in my work, it’s still subtly influencing how I write. Continue reading “The Free Scientific Resource: Evaluating the Accuracy of Wikipedia”
Salmonella. Streptococcus. Shigella. The most well-known bacteria are those that cause disease. Our relationship with them is one of combat. With good reason, we look for ways to avoid encountering them and to eliminate them when we do meet.
But not all bacteria are bad for us. Of course we have known for years that we are colonized by harmless bacteria, but recently, studies on the human microbiome have revealed many surprising things about these bacterial tenants. Studies are showing that the teeming multitudes of organisms living in and on the human body are not just harmless bystanders, but complex, interrelated communities that can have profound effects on our health.
Three studies published last week in Science add more to the growing body of microbiome surprises, showing that certain gut bacteria are not only good for us, but may even be required for the effectiveness of some anti-cancer immunotherapies.
Recently, I stumbled upon a few new discoveries that I would have guessed had already been figured out. These discoveries were surprising to me because they fell into the category of “obviously someone else knows this,” even though I didn’t—you know, the stuff you would just do a quick Google search to find out about.
Anyway, it made me reflect on the world we live in, filled with endless information. At times, it seems as if we know it all (at least all the obvious stuff), which can stifle discovery by limiting the sources from which we seek new information. It can appear futile to embark upon research in established fields. But sometimes discoveries occur when you look in familiar places from a new vantage point.
Today’s blog illustrates how seeing science in new ways can lead to this type of unexpected discovery.
Sometimes seeing science is about how you are looking.
The first discovery that got my attention was in an article that described the use of drones and Google Earth by archaeologists to discover a monument made of stone hidden below the sand at a World Heritage Site in Petra, Jordan. This is one of the most visited and well-studied archaeological sites in the world. Yet, a huge structure had remained undiscovered despite continual investigation of the site.
Have you ever noticed that after a good long day outdoors, maybe hiking, at the beach or even working in the yard, you feel really strong and healthy, maybe even more relaxed than after an indoor session in front of the telly or computer? Maybe a February trip to someplace sunny like Mexico or the Canary Islands has given you renewed zest for your normal tasks?
While rest and a change of scenery is never a bad thing, time outdoors and in the sunshine might have gained for you something more than rest and relaxation. If it included a little UVB irradiation, your time outdoors may have increased your serum vitamin D level. And though it’s been presumed for years, we now have proof that higher serum vitamin D3 levels correlate with a decreased incidence of certain cancers. Continue reading “Vitamin D: Power in Cancer Prevention?”
Zika virus has been in the news recently due to growing concerns about its global spread. If you have never heard of Zika virus before, you are not alone. Although first discovered in the 1940s, Zika has not been the subject of much study as infection is considered rare and the symptoms mild. However, all this has changed in recent months due to the rapid spread of the virus in Latin America, where it has been associated with an increased incidence of microcephaly, a severe birth defect where babies are born with underdeveloped brains. Although the connection of Zika with microcephaly is not yet proven, the circumstantial evidence is strong, leading the World Health Organization to declare the spread of Zika virus an international public health emergency earlier this week. Continue reading “Zika: Another RNA Virus Emerges”
The last weeks have seen the publication of the traditional lists and retrospectives summing up the key events and influential people of 2013—we have the “Person of the Year”, the top news stories of the year, the best songs of the year, and so on. Many of the major science publishers have also compiled their perspectives on the top science news stories of 2013. So what were the most memorable science stories of the year?
Although it is more than 200 years since Jenner’s pioneering work on vaccination, there are still many infectious diseases that resist the development of effective vaccines. Somewhat shockingly, despite years of research effort, there are still no highly effective vaccines against human parasitic diseases. Malaria, the most problematic of these, kills more than half a million people each year—many of these infants and children, qualifying the mosquito that transmits the parasite as one of the most dangerous creatures on earth. Not surprisingly then, recent hopeful news of an anti-malaria vaccine that appears to protect against the disease has been greeted with enthusiasm.
The search for an effective anti-malaria vaccine has been fraught with difficulty due to the complex life cycle of the parasite (Plasmodium falciparum and other Plasmoduim species), compounded by its propensity to change its surface composition and develop resistance to various treatment efforts. The parasite thus presents an ever-changing target for treatment efforts. In the absence of an effective vaccine, anti-malarial efforts have been dependent on drug treatment (also liable to development of resistance), eradication programs, and preventive measures such as insecticide-laced mosquito netting. Continue reading “Hope for an Anti-Malaria Vaccine”
Every scientific paper is the story of a journey from an initial hypothesis to a final conclusion. It may take months or years and consists of many steps taken carefully one at a time. The experiments are repeated, the controls verified, the negative and positive results analyzed until the story finally makes sense. Sometimes the end of the story confirms the hypothesis, sometimes it is a surprise. A paper published last week in Cell describes a study where a team of researchers investigating one problem in basic biology (how one component of a signaling complex works), found an unexpected and potentially significant application in a different field (cancer research).
The paper, published in the June 6 issue of Cell, describes a previously unknown interaction between two cellular proteins—the transcription factor HIF1A and the cyclin-dependent kinase CDK8—in the regulation of genes associated with cellular survival under low-oxygen conditions. An accompanying press release describes how the discovery of a role for CDK8 in this process may have implications for cancer research, as CDK8 may be a potential target for drugs to combat “hypoxic” tumors. Continue reading “Basic Biology Matters”