Science News for April the First

This year I have the uncommon honor of blogging on April 1st. For those people who do not know, the first day of April is called April Fool’s Day where jokes, practical and otherwise, abound and news headlines may or may not be disingenuous. For example, Google is introducing Google Nose to improve and share olfactory experiences. Can you spot which of the following science news stories were created for the holiday?

The Desinovian genome that was recently sequenced was actually found to be a close relative to that of Neandertals. In fact, the close alignment and identity of the two genome sequences means that these two separate designated ancestors of humans are, in fact, most likely the same species. This means that Neandertals had a wider continental distribution than first thought, indicating a greater likelihood of their genetics becoming part of modern Homo sapiens.

In an interesting role reversal, antibiotic-sensitive bacteria are mounting a reproductive blitz to take back territory ceded to antibiotic-resistant bacteria like methicillin-resistant Staphylococcus aureus (MRSA), New Delhi metallo-β-lactamase-(NDM-1) producing strain of Klebsiella pneumonia and vancomycin-resistant enterococci (VRE). The newest territorial battleground is the human body. One woman recovered after infection with multidrug-resistant MRSA when treatment with ampicillin cleared up the infection in a week.

Bacteria have also taken the headline in a new way: gut microbiota from mice that had slimmed down after gastric bypass surgery were transplanted into obese mice, inducing weight loss without surgery. This research is the just latest in studies looking at how the microbes in the gut influence the entire organism. If this research can be replicated in humans, gastric bypass surgery may lose out to a knifeless solution.

A Cup of Coffee, Hold the Rust

Rust on the underside of a coffee leaf.
Rust on the underside of a coffee leaf. Image used courtesy of Wikipedia.

While at my desk early in the day last week, one headline struck me as particularly troubling: “Coffee Rust Regains Foothold”.

Reports from the Institute of Coffee of Costa Rica estimate that the latest coffee outbreak may cut by 50% the 2013-14 coffee harvest in that country. Coffee specialists in the U.S. are calling it the worst outbreak of rust in Mexico and Central America since rust arrived in the region, 40-some years ago.

And in Kenya, Africa, coffee rust has been described as causing ever-greater problems, even with Kenyan coffee varieties resistant to rust being grown.

Several Central American governments are enacting special legislation to fund projects against spread of the fungus.

It’s early February and in this little corner of the world, times seem tough. We are suddenly (although typically, for southern Wisconsin, USA) getting regular snowfalls: 3” this day, 6” a day later. It adds up to a lot of shoveling.  There is nothing like a fresh snowfall and 30 minutes of shoveling to slow the morning commute. Continue reading “A Cup of Coffee, Hold the Rust”

Sonnets in DNA

William ShakespeareFor sixty years now, scientists have studied the role of DNA as a vehicle for the storage and transmission of genetic information from generation to generation. We have marveled at the capacity of DNA to store all the information required to describe a human being using only a 4-letter code, and to pack that information into a space the size of the nucleus of a single cell. A letter published last week in Nature exploits this phenomenal storage capacity of DNA to archive a quite different kind of information. Forget CDs, hard drives and chips, the sum of human knowledge can now be stored in synthetic DNA strands. The Nature letter, authored by scientists from the European Bioinformatics Institute in Cambridge, UK, and Agilent Technologies in California, describes a proof-of-concept experiment where synthetic DNA was used to encode Shakespeare’s Sonnets, Martin Luther King’s “I Have a Dream” speech, a picture of the Bioinformatics Institute, and the original Crick and Watson paper on the double-helical nature of DNA. Continue reading “Sonnets in DNA”

Science Stories for Halloween

In keeping with our tradition at Promega Connections, we have put together a “Halloween-themed” blog for you. This year we compiled a list of science-related stories that we felt had a certain spooky air about them. Enjoy! And, if you have other stories to add to this list, leave us a comment.

  • Zombie Bees: In January 2012, Andrew Core and colleagues published an article in PLOS ONE describing “zombie” honey bees. With the host of pathogens and pesticides that can harm honey bee colonies, loss of honey bee colonies and rapid declines of honey bee populations world wide, perhaps the worst news bee keepers could get is the description of a new bee zombie parasite. Continue reading “Science Stories for Halloween”

My Microbiome Made Me Do It

When I was in school I learned that there were two different kinds of bacteria, the nasty ones (pathogens) that could make you sick and the nice ones (commensals), which simply colonized you and did nothing much except occupy a spot that could otherwise be taken up by a pathogen. Any role for those commensal bacteria in health and disease was assumed to be no more than that of a harmless squatter. In recent years, studies of this benign microbial population (microbiome studies) have begun to reveal many more intriguing details about how they affect our health and wellbeing. Maybe it’s not so surprising that “good” bacteria could be good for our health—but could they actually affect how we behave? This month, a review in Science summarized new findings that indicate that this is indeed the case—at least for certain animal populations. Could it be true for humans as well? Could our colonizing organisms actually influence how we feel and what we do? Continue reading “My Microbiome Made Me Do It”

It’s a Jungle in There: ENCODE and the Redefinition of the Gene

September 5th saw the simultaneous publication of more than 30 papers in Nature, Genome Research and Genome Biology detailing the findings of the ENCODE project (Encyclopedia of DNA Elements)—an international collaborative research effort involving the work of more than 400 scientists in 32 groups over the last eight years. Building on the work of the human genome project, the goal of the ENCODE project was to catalog and describe all the functional elements in the human genome.

The human genome project revealed the surprising fact that only 1% of our genome encodes proteins–a mere 20,000 genes. The function of the other 99% of our DNA remained a mystery. The ENCODE project was established in 2003 to survey and catalog these unknown DNA regions in a systematic manner. Continue reading “It’s a Jungle in There: ENCODE and the Redefinition of the Gene”

Thermometers in Wine, the Edge of the Solar System and Redefining Junk DNA: Science News of the Week

Science keeps on producing new discoveries every week. It can be difficult to keep up with the latest news even when it is part of your job. There were a few science stories that caught my attention this week so I thought I would share them.

Galilean Thermometer Not So Galilean” was a surprising news item. I love my Galileo thermometer received as a Christmas gift several years ago. However, as Peter Loyson’s commentary in the Journal of Chemical Education points out, Galileo Galilei invented a thermometer but it was based on air. The one attributed to him was created by a Florentine group of academics and technicians founded by the Grand Duke Ferdinand II and his brother Leopoldo. And those first thermometers? Used wine to float the little glass balls.

Voyager 1, which just turned 35 on September 5, and Voyager 2 are pushing at the boundaries of our solar system as well as our understanding of space. In fact, NASA is saying that Voyager 1 was expected to pass through the heliopause, the edge that defines the end of the influence of our sun and the beginning of true interstellar space, but recent data indicated that this edge is further than we imagined. In fact, it could lie seven years beyond Voyager 1’s current position, and the battery in each Voyager estimated to deplete between 2020 and 2025. Still, these two small satellites have boldly gone beyond their initial mission to explore the far reaches of space and are still sending data back to our humble Earth.

Sequencing the human genome was an accomplishment but just this week, the scientists involved in the Encyclopedia of DNA Elements (ENCODE) project published 30 papers in Nature and other journals (summarized here). With the complete human sequence in hand, most scientists thought the items of interest in the genome were the genes, the coding regions. But as researchers started to dig into the data and use it for their experiments, it became evident understanding the genome was more complex than the sequence. The ENCODE project is a consortium of scientists that wanted to understand the entire genome and ended up finding that the 2% that encodes proteins is controlled by those sequences between genes nicknamed “junk DNA”. It is an incredible effort that has implications across aging and cancer, and ENCODE claims it can assign functions to 80% of the genome.

Seeing the Potential

neuronal signalingI had never heard of Halorubrum sodomense until a few days ago. It’s name describes it pretty well, it is a salt-tolerant (Halophilic) organism that contains the red-colored photosynthetic pigment archaerhodopsin, and it was originally isolated from the region of Sodom near the Dead Sea. It’s an organism that is well-known only to those with reason to study it. Many of the rest of us will never have cause to say its name, or to even remember it, and may even occasionally wonder why it is studied at all.

Halorubrum sodomense was in the news recently because a genetically engineered form of its rhodopsin was used to create a method that lights up mammalian neurons as they fire. This exciting development was reported in a paper by Kralj et al, published in the Nov 27 issue of Nature Methods. Continue reading “Seeing the Potential”

The Search for New Antibiotics: Looking for Achilles’ Heel (Again)

Some of the first available doses of penicillin were used to treat allied soldiers wounded on D-Day. It was the end of one war, but just the beginning of another–one that has gone on for a long time. The story of the development of antibiotics, and the emergence of resistant bacteria, followed by the renewed search for new antibiotics, seems neverending. As soon as a new antibiotic is discovered, it seems only a matter of time before a resistance mechanism emerges, and remaining one step ahead of the bugs can seem like a relentless challenge. Continue reading “The Search for New Antibiotics: Looking for Achilles’ Heel (Again)”

Quorum Sensing in Bacteria: How a Picture can be Worth a Thousand Words

Increasingly, multimedia and video are being used in addition to traditional delivery methods to communicate scientific findings. Journals such as PLoS ONE, Cell, Nature and others often use video to either showcase particular articles, or offer authors the opportunity to include multimedia elements as part of their article. Some subjects lend themselves better to video delivery than others. Every so often a video report comes along that perfectly complements the content of the associated paper, illustrating the power of video to enhance communication of research findings.

In my opinion, the effective use of video to highlight results is beautifully illustrated by the report below, highlighting the publication “A synchronized quorum of genetic clocks” by Danino et al, which was published in Nature this week.

[youtube=http://www.youtube.com/watch?v=pnjdAr4EjI0]
Continue reading “Quorum Sensing in Bacteria: How a Picture can be Worth a Thousand Words”