Category Archives: Students

Items for students and others, interested in learning about science and engineering and the application of science in our lives. We post many of the general interest items here.

Parasites in the Gut Help Develop a Healthy Immune System

It has long been known that microbes in the gut help to develop a healthy immune system, hence the rise in popularity of probiotic yoghurts that encourage ‘friendly’ bacteria. But new research by Professors Richard Grencis and Ian Roberts shows that larger organisms such as parasitic worms are also essential in maintaining our bodily ‘ecosystem’. “The worms have been with us throughout our evolution and their presence, along with bacteria, in the ecosystem of the gut is important in the development of a functional immune system.”

Parasite Rex is a great book, I have written about previously looking at parasites and their affect on human health.

Professor Grencis adds: “If you look at the incidence of parasitic worm infection and compare it to the incidence of auto-immune disease and allergy, where the body’s immune system over-reacts and causes damage, they have little overlap. Clean places in the West, where parasites are eradicated, see problems caused by overactive immune systems. In the developing world, there is more parasitic worm infection but less auto-immune and allergic problems.

“We are not suggesting that people deliberately infect themselves with parasitic worms but we are saying that these larger pathogens make things that help our immune system. We have evolved with both the bugs and the worms and there are consequences of that interaction, so they are important to the development of our immune system.”

Whipworm, also known as Trichuris, is a very common type of parasitic worm and infects many species of animals including millions of humans. It has also been with us and animals throughout evolution. The parasites live in the large intestine, the very site containing the bulk of the intestinal bacteria.

Heavy infections of whipworm can cause bloody diarrhoea, with long-standing blood loss leading to iron-deficiency anaemia, and even rectal prolapse. But light infections have relatively few symptoms.
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Students Will Spend Year Doing Career-Changing Research Thanks to HHMI

This year, 116 medical, dental, and veterinary students from 47 schools across the country will take a break from memorizing molecular metabolism and studying drug interactions to spend a year in a lab doing hands-on research. The break from regular coursework, funded through a $4 million Howard Hughes Medical Institute (HHMI) initiative, is intended to give students an opportunity to immerse themselves in science and consider whether they want to pursue a career as a physician-scientist.

Nearly 500 medical students applied for the research year through the HHMI-National Institutes of Health (NIH) Medical Research Scholars and HHMI Medical Research Fellows programs. Both efforts seek to strengthen and expand the pool of medically-trained researchers. The funding HHMI provides is a great resource.

“We want medical, dental, and veterinary students to become immersed in the life of academic science for at least a year. And we hope they get so engaged in the process and life of scientific research that they will decide to continue it for the rest of their lives,” says Peter Bruns, HHMI’s vice president for grants and special programs. “We need more doctors who do basic research to improve human health.”

As part of its commitment to fostering the translation of basic research discoveries into improved diagnoses and treatments, HHMI has developed a range of programs to nurture the careers of researchers who bridge the gap between clinical medicine and basic science. In addition to the programs for medical students, the Institute supports medical training for Ph.D. students in the basic sciences and has made specific efforts to fund top physician-scientists as HHMI investigators.

The medical research scholars and fellows programs are open to medical, dental, and veterinary students enrolled in U.S. schools. Most have completed the second or third year of their professional program when they spend a year working in a lab either at the NIH or at an academic medical center or research university they select. During the last 25 years, more than 2,100 students have participated.

The HHMI Medical Research Fellowships program allows medical, dental, and veterinary students to pursue biomedical research at a laboratory anywhere in the United States except the NIH campus in Bethesda. Each student submits a research plan to work in a specific lab with a mentor they have identified. Since 1989, about 1,200 students have participated.

This year, 74 students from 26 medical schools and two veterinary schools were chosen as fellows from a pool of 274. While most students elect to stay at their home institution to do their research, this year 17 fellows will work in labs at a different school. Their research topics include schizophrenia, wound healing, organ development, and many other important biological questions.

The HHMI-NIH Research Scholars program was established in 1985 to encourage medical students to pursue research by allowing them to take a year off from their medical studies. The program has since been expanded to include dental and veterinary students. It has enabled about 1,000 students to work in NIH labs.

Students selected as research scholars often enter the program with only a general idea of what type of research they would like to do. As soon as they are accepted, they begin researching the more than 1,100 laboratories at NIH. They meet with a number potential mentors before finalizing which project to pursue under the guidance of their NIH advisor and HHMI’s staff. The students are sometimes called “cloister scholars” because they live in apartments or dorm-style rooms in a refurbished cloister on the NIH campus in Bethesda.

This year, 42 students from 28 medical schools and one veterinary school were chosen as research scholars. More than 200 students from 93 schools applied.

All present-day Life on Earth Has A Single Ancestor

All present-day life arose from a single ancestor

All life on Earth shares a single common ancestor, a new statistical analysis confirms.
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Because microorganisms of different species often swap genes, some scientists have proposed that multiple primordial life forms could have tossed their genetic material into life’s mix, creating a web, rather than a tree of life.
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A universal common ancestor is at least 10^2,860 times more probable than having multiple ancestors, Theobald calculates.
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For his analysis, Theobald selected 23 proteins that are found across the taxonomic spectrum but have structures that differ from one species to another. He looked at those proteins in 12 species – four each from the bacterial, archaeal and eukaryotic domains of life.

Then he performed computer simulations to evaluate how likely various evolutionary scenarios were to produce the observed array of proteins. Theobald found that scenarios featuring a universal common ancestor won hands down against even the best-performing multi-ancestor models.

Very interesting. Surprising too. As the article points out this doesn’t mean all life ever on Earth evolved from the single ancestor – life that has gone extinct could be from outside this single “tree.”

Variation in Human DNA

Variation on the order of thousands to hundreds of thousands of DNA’s smallest pieces – large swaths varying in length or location or even showing up in reverse order – appeared 4,205 times in a comparison of DNA from just four people.

Those structural differences popped into clear view through computer analysis of more than 500 linear feet of DNA molecules analyzed by the powerful genome mapping system developed over nearly two decades by David C. Schwartz, professor of chemistry and genetics at UW-Madison.

“We probably have the most comprehensive view of the human genome ever,” Schwartz says. “And the variation we’re seeing in the human genome is something we’ve known was there and important for many years, but we haven’t been able to fully study it.”

To get a better picture of those structural variations, Schwartz and his team developed the Optical Mapping System, a wholly new type of genome analysis that directly examines millions of individual DNA molecules.

“Our newer genome analysis systems, if commercialized, promise genome analysis in one hour, at under $1,000,” Schwartz says. “And we require that high speed and low cost to power the new field of personal genomics.”

Read full press release

Whales Evolved in the Blink of an Eye, Only 5 Million Years

Whales Evolved in the Blink of an Eye

Whales’ sizes stretch the imagination from the 100-foot (30-meter) long blue whale – the largest animal to have ever existed – to a small species about the size of a dog.
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Around 35 million years ago, when modern whales began to appear in the ocean, whale evolution ignited. Whales began as basically similar body types and evolved into everything from porpoises to blue whales over the next 5 million years, said study lead author Graham Slater of UCLA. “Five million years is like the blink of an eye,” Slater told LiveScience.

The finding supports what’s known as the explosive radiation hypothesis. The idea is that a few key traits allowed the earliest ancestors of modern cetaceans – marine mammals, including whales, dolphins and porpoises – to explore new ways of living. Once these ancestors branched out into a new body form, they stayed the course.

The key traits credited with the explosive evolution include sonar, large brains, baleen (the stringy looking stuff across some whales’ mouths that filters small animals from sea water), and complex sociality.

All About Circuits

All About Circuits is an online textbook covering electricity and electronics. Topics covered include: Basic Concepts of Electricity’ OHM’s Law; Electrical Safety; Series and Parallel Circuits; Physics of Conductors and Insulators; Solid-State Device Theory; Binary Arithmetic; Logic Gates; Switches; Digital Storage? It is a great resource. Enjoy.

Mycoremediation and its Applications In Oil Spills

The webcast shows a talk by mycologist Paul Stamets on Bioremediation with Fungi (an Excerpt from Mushrooms as Planetary Healers). In response he to the British Petroleum/Halliburton oil spill he posted a message, Fungi Perfecti: the petroleum problem

Various enzymes (from mushroom mycoremediation) breakdown a wide assortment of hydrocarbon toxins.
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My work with Battelle Laboratories, in collaboration with their scientists, resulted in TAH’s (Total Aromatic Hydrocarbons) in diesel contaminated soil to be reduced from 10,000 ppm to < 200 ppm in 16 weeks from a 25% inoculation rate of oyster (Pleurotus ostreatus) mycelium, allowing the remediated soil to be approved for use as landscaping soil along highways. [paper]
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Aged mycelium from oyster mushrooms (Pleurotus ostreatus) mixed in with ‘compost’ made from woodchips and yard waste (50:50 by volume) resulted in far better degradation of hydrocarbons than oyster mushroom mycelium or compost alone.
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Oyster mushrooms producing on oil contaminated soil (1–2% = 10,000–20,000 ppm)… Soil toxicity reduced in 16 weeks to less than ~ 200 ppm, allowing for plants, worms and other species to inhabit whereas control piles remained toxic to plants and worms.
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New crop of mushrooms form several weeks later [after contaminating with oil]. The spores released by these mushrooms have the potential – as a epigenetic response – to pre-select new strains more adaptive to this oil-saturated substrate.
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I proposed in 1994 that we have Mycological Response Teams (MRTs) in place to react to catastrophic events, from hurricanes to oil spills. We need to preposition composting and mycoremediation centers adjacent to population centers
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On a grand scale, I envision that we, as a people, develop a common myco-ecology of consciousness and address these common goals through the use of mycelium. To do so means we need to spread awareness and information. Please spread the word of mycelium.

A Breakthrough Cure for Ebola

A breakthrough cure for Ebola By Steven Salzberg

Last week, in what may be the biggest medical breakthrough of its kind in years, a group of scientists published results in The Lancet describing a completely new type of anti-viral treatment that appears to cure Ebola. They report a 100% success rate, although admittedly the test group was very small, just 4 rhesus monkeys.

This is a breakthrough not only because it may give us a cure for an uncurable, incredibly nasty virus, but also because the same method might work for other viruses, and because we have woefully few effective antiviral treatments. We can treat bacterial infections with antibiotics, but for most viruses, we have either a vaccine or nothing. And a vaccine, wonderful as it is, doesn’t help you after you’re already infected.

The scientists, led by Thomas Geisbert at Boston University, used a relatively new genomics technique called RNA interference to defeat the virus. Here’s how it works.
First, a little background: the Ebola virus is made of RNA, just like the influenza virus. And just like influenza, Ebola has very few genes – only 8. One of its genes, called L protein, is responsible for copying the virus itself. Two others, called VP24 and VP35, interfere with the human immune response, making it difficult for our immune system to defeat the virus.

Geisbert and his colleagues (including scientists from Tekmira Pharmaceuticals and USAMRIID) designed and synthesized RNA sequences that would stick to these 3 genes like glue. How did they do that? We know the Ebola genome’s sequence – it was sequenced way back in 1993. And we know that RNA sticks to itself using the same rules that DNA uses. This knowledge allowed Geisbert and colleagues to design a total of 10 pieces of RNA (called “small interfering RNA” or siRNA) that they knew would stick to the 3 Ebola genes. They also took care to make sure that their sticky RNA would not stick to any human genes, which might be harmful. They packaged these RNAs for delivery by inserting them into nanoparticles that were only 81-85 nanometers across.
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USA Science And Engineering Kavli Video Contest

Do you think Science is cool? Do you want to share your passion for science with others? Here is your chance to inspire thousands of people to be more curious, and to care about science & engineering the way you do: create a short video that explores the question “Why is Science Cool?”

We are seeking videos that are creative, surprising, and “contagious” in terms of spreading your enthusiasm about science to others. Videos might explore a scientific concept, show us the wonders of nature, give us a glimpse into the future, show us what scientific discovery has done for us in the past or will do for us in the future, introduce us to a great scientist or engineer, tell us why you think science is so cool or simply show us why we should care about science and/or engineering.

1st prize: $1,000 (to the school or science club); plus $500 electronics gift certificate for the student (or student group); plus a travel stipend to travel to Washington DC for the Expo!

In addition, the winning videos will be screened during the USA Science & Engineering Festival Expo on the National Mall in Washington DC on October 23 and 24, 2010 and at other key Festival events.

Find out how to submit a video.

Home Engineering: Bird Feeder That Automatically Takes Photos When Birds Feed

During a trip to the Smithsonian last week I found this great home engineering project. Kayty Himelstein and Amy Darr were frustrated: birds came to their bird feeder while they were away at school, so the girls never got to see them. They decided to build a bird feeder that automatically takes pictures of all the birds that came to the feeder. I believe, they used Lego Mindstorms as part of building it.