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.

Amazon Molly Fish are All Female

No sex for all-girl fish species

A fish species, which is all female, has survived for 70,000 years without reproducing sexually, experts believe.
…
The species, found in Texas and Mexico, interacts with males of other species to trigger its reproduction process. The offspring are clones of their mother and do not inherit any of the male’s DNA. Typically, when creatures reproduce asexually, harmful changes creep into their genes over many generations.
…
One theory is that the fish may occasionally be taking some of the DNA from the males that trigger reproduction, in order to refresh their gene pool.

Dr Laurence Loewe, of the university’s School of Biological Sciences, said: “What we have shown now is that this fish really has something special going on and that some special tricks exist to help this fish survive. “Maybe there is still occasional sex with strangers that keeps the species alive. Future research may give us some answers.”

He added that their findings could also help them understand more about how other creatures operate. “I think one of the interesting things is that we are learning more about how other species might use these tricks as well,” he said. “It might have a more general importance.”

$60 Million for Science Teaching at Liberal Arts Colleges

HHMI Awards $60 Million to Invigorate Science Teaching at Liberal Arts Colleges

A year ago, the Howard Hughes Medical Institute issued a challenge to 224 undergraduate colleges nationwide: identify creative new ways to engage your students in the biological sciences.

Now 48 of the nation’s best undergraduate institutions will receive $60 million to help them usher in a new era of science education. This includes the largest number of new grantees in more than a decade; more than a quarter have never received an HHMI grant before.

Colleges in 21 states and Puerto Rico will receive $700,000 to $1.6 million over the next four years to revitalize their life sciences undergraduate instruction. HHMI has challenged colleges to create more engaging science classes, bring real-world research experiences to students, and increase the diversity of students who study science.
…
Creating interdisciplinary science classes and incorporating more mathematics into the biology curriculum were among the major themes proposed by the schools. Many schools will also allow more students to experience research through classroom-based courses and summer laboratory programs.
…
HHMI is the nation’s largest private supporter of science education. It has invested more than $1.2 billion in grants to reinvigorate life science education at both research universities and liberal arts colleges and to engage the nation’s leading scientists in teaching. In 2007, it launched the Science Education Alliance, which will serve as a national resource for the development and distribution of innovative science education materials and methods.

Potential Viral Therapy for Difficult Cancers

Potential viral therapy weapon for difficult cancers is safe and effective in study

Combining a herpes virus genetically altered to express a drug-enhancing enzyme with a chemotherapy drug effectively and safely reduced the size of highly malignant human sarcoma grafted into mice. This new finding may add to the growing arsenal of so called oncolytic viruses under development as novel cancer treatments, especially for difficult, inoperable tumors
…
“Based on these findings and other preclinical studies, we expect oncolytic viral therapy will be one additional treatment modality available in the future for oncologists,” Dr. Cripe said. “The challenge over the next decade will be determining which viruses work best for which cancers, at what doses, schedules, routes of administration, and in what combinations with other treatments.”

E. Coli Individuality

Expressing Our Individuality, the Way E. Coli Do by Carl Zimmer

A good counterexample is E. coli, a species of bacteria that lives harmlessly in every person’s gut by the billions. A typical E. coli contains about 4,000 genes (we have about 20,000). Feeding on sugar, the microbe grows till it is ready to split in two. It makes two copies of its genome, almost always managing to produce perfect copies of the original. The single microbe splits in two, and each new E. coli receives one of the identical genomes. These two bacteria are, in other words, clones.
…
A colony of genetically identical E. coli is, in fact, a mob of individuals. Under identical conditions, they will behave in different ways. They have fingerprints of their own.
…
E. coli appears to follow a universal rule. Other microbes exploit noise, as do flies, worms and humans. Some of the light-sensitive cells in our eyes are tuned to green light, and others to red. The choice is a matter of chance. One protein may randomly switch on the green gene or the red gene, but not both.

In our noses, nerve cells can choose among hundreds of different kinds of odor receptors. Each cell picks only one, and evidence suggests that the choice is controlled by the unpredictable bursts of proteins within each neuron. It’s far more economical to let noise make the decision than to make proteins that can control hundreds of individual odor receptor genes.

Identical genes can also behave differently in our cells because some of our DNA is capped by carbon and hydrogen atoms called methyl groups. Methyl groups can control whether genes make proteins or remain silent. In humans (as well as in other organisms like E. coli), methyl groups sometimes fall off of DNA or become attached to new spots. Pure chance may be responsible for changing some methyl groups; nutrients and toxins may change others.

Viruses Eating Bacteria

All the World’s a Phage by John Travis:

“Believe it or not, nobody had looked before,” says Suttle. “On average, there are 50 million viruses per milliliter in seawater. The question is, What the heck they’re doing there?” Microbiologists then documented similar, and even higher, concentrations of phages in soil samples. This led to estimates of 10³¹ bacteriophages worldwide, a staggeringly large number that many scientists initially dismissed. “We can’t wrap our brains around it,” says Pedulla. “If phages were the size of a beetle, they would cover the Earth and be many miles deep.”
…
According to estimates put forth by Suttle, phages destroy up to 40 percent of the bacteria in Earth’s oceans each day.
…
The students collected soil from barnyards, gardens, and even the monkey pit at the Bronx Zoo. The scientists then taught the students how to isolate a bacteriophage from the soil by growing the viruses in Mycobacterium smegmatis, a harmless bacterial relative of the microbe that causes tuberculosis. “We guarantee them that the bacteriophage they find will never have been discovered before. We know that because the diversity is so high, and we’ve never isolated the same bacteriophage twice,” says Hatfull.

In the April 18 Cell, Hatfull and his professional and teenage collaborators describe the genomes of 10 soil-dwelling bacteriophages that they had isolated. Of the more than 1,600 genes that the team identified, about half are novel, that is, they don’t match any previously described genes in any other organism.

Science is full of amazing new frontiers. Some other amazing stuff: Thinking Slime Moulds – Tracking the Ecosystem Within Us – Retroviruses – Energy Efficiency of Digestion – One Species’ DNA Discovered Inside Another’s

Sudden Oak Death

Sudden Oak Death pathogen is evolving, says new study that reconstructs the epidemic

The pathogen responsible for Sudden Oak Death first got its grip in California’s forests outside a nursery in Santa Cruz and at Mt. Tamalpais in Marin County before spreading out to eventually kill millions of oaks and tanoaks along the Pacific Coast, according to a new study led by researchers at the University of California, Berkeley. It provides, for the first time, evidence of how the epidemic unfolded in this state.
…
The study, scheduled to appear later this month in the online early edition of the journal Molecular Ecology, also shows that the pathogen is currently evolving in California, with mutant genotypes appearing as new areas are infested.
…
The most likely scenario, said Garbelotto, is that the pathogen arrived in California through the nursery trade, and that it then spread from the nursery in Santa Cruz to trees bordering the facility. While the site at Mt. Tamalpais is not adjacent to a nursery, there is anecdotal evidence of frequent use of ornamental plants from nurseries in landscaping projects in the area, said Garbelotto.

Pigs Instead of Pesticides

photos of pigs in an orchard

Apple Farmers Use Pigs Instead of Pesticides [the broken link was removed]

Jim Koan has a 120-acre apple farm in Flushing, MI. Plagued by the Plum Curculio Beetle that lays its eggs in apples and makes the fruit drop too early from trees, Koan could have used frequent sprays of pesticides for years to get rid of the beetles, or he could use pigs. He tried chickens and guineas, but they weren’t hard enough workers and the guineas were taken away by hawks. He contemplated sheep, too, but in the end, hard-working pigs, too big for any hawk or coyote to steal, were the best bet.

Now he has a group of pigs who shuffle through the orchards when the apples infected with beetles start to fall. They eat the apples and the eggs that would have spelled disaster for next year’s crop, and clear the ground and eat weeds in the process. The pigs make short work of an apple orchard, eating every last contaminated apple. Once the pigs have solved the beetle problem, Koan plans to sell them as organic pork.

Very nice. I like the idea of reducing the use of chemicals in general and it is especially nice when the solution shows that one person’s problem is a pig’s food.

via: It’s the Only One We Have [the broken link was removed], where the photo is from also

Wabash Valley, Illinois Earthquakes

USGS on the recent earthquakes occurred in the Wabash Valley Seismic

These earthquakes occurred in the Wabash Valley Seismic zone. The earthquakes in this zone are scattered over a large area of southeastern Illinois and southwest Indiana. The zone had at least eight prehistoric earthquakes over the past 20,000 years with estimated magnitudes ranging from about 6.5 to 7.5, based on geologic evidence. Earthquakes of the size of the recent quake (Mw 5.2) can produce smaller aftershocks over the following days. A few might be large enough to be felt. Typically, earthquakes of this size (Mw 5.2) can cause light damage within a few tens of miles from the epicenter. Central and eastern US earthquakes generally shake areas about 10 times as large as those that occur in California. It is not surprising that this earthquake was felt as far south as Florida.

The Wabash Valley Seismic zone is adjacent to the more seismically active New Madrid seismic zone on the seismic zone’s north and west. The recent earthquake is also within the Illinois basin – Ozark dome region that covers parts of Indiana, Kentucky, Illinois, Missouri, and Arkansas and stretches from Indianapolis and St. Louis to Memphis. Moderately frequent earthquakes occur at irregular intervals throughout the region. The largest historical earthquake in the Illinois Basin region (magnitude 5.4) damaged southern Illinois in 1968. Moderately damaging earthquakes strike somewhere in the region each decade or two, and smaller earthquakes are felt about once or twice a year.

Earthquakes in the central and eastern U.S., although less frequent than in the western U.S., are typically felt over a much broader region. East of the Rockies, an earthquake can be felt over an area as much as ten times larger than a similar magnitude earthquake on the west coast.

Amazing Designs of Life

The More We Know About Genes, the Less We Understand by Carl Zimmer

All living things, ourselves included, turn genes on and off in a similar way, by making switch-like proteins called transcription factors. And as scientists have identified more of these, they’ve discovered something remarkable: They form a chain of command. The job of some transcription factors is to switch others on and off, and they in turn are controlled by other transcription factors. Even a seemingly simple microbe like E. coli has an impressive hierarchy. Just nine genes rule over about half of the 4,000-odd genes in E. coli.

E. coli’s network allows it to respond quickly to the challenges it meets, from starvation to heat to the loss of oxygen. It can rapidly reorganize itself, switching on hundreds of genes and switching off hundreds of others. What makes this network all the more impressive are the feedback loops that keep it from spinning out of control. When one gene switches on, for example, it may make a protein that shuts down the gene that switched it on in the first place.

Yet even as scientists uncover this network, they discover yet another mystery. In the latest issue of Nature, scientists reported an experiment in which they wreaked havoc with E. coli’s network. They randomly added new links between the transcription factors at the top of the microbe’s hierarchy. Now a transcription factor could turn on another one that it never had before. The scientists randomly rewired the network in 598 different ways and then stepped back to see what happened to the bacteria.

You might expect that they all died. After all, if you were to pop open the back of an iPod and start linking its components together in random ways, you’d expect it to crash. But that’s not what happened.

About 95 percent of the rewired bacteria did just fine with their new networks. They went on with their lives, feeding, growing and dividing. Some even performed better than microbes with the original wiring, under some conditions.

Biodegradable Plastic Bags and Bottles

researchers look to make environmentally friendly plastics

Every year, more than 30 billion water bottles are added to America’s landfills, creating a mountainous environmental problem. But if research at Missouri University of Science and Technology is successful, the plastic bottles of the future could literally disappear within four months of being discarded.

The Missouri S&T research team is constructing new breeds of biodegradable and bioavailable plastics in an effort to reduce the tons of plastic waste that ends up in the nation’s landfills each year. Bioavailable plastics contain substances that can be absorbed by living systems during their normal physiological functions.

By combining and modifying a variety of bio-based, oil-based and natural polymers, the team seeks to create optimal blends that can be used to make agricultural films, bottles, biomedical and drug delivery devices, and more.
…
As polylactic acid degrades, the material reacts with water to decompose into small molecules, which are then mineralized into water and carbon dioxide.

“In general, the main end products of polymer degradation are water and carbon dioxide,” Shahlari explains. “Polylatic acid has the potential of replacing the regular water bottles, and we anticipate that our research could be incorporated into that field too.

It sure seems like they are saying these would really biodegrade. Plastic bags can photodegrade where they break down into small bits of plastic that might be hard to see but are still toxic that can be eaten by animals, and us. As one would figure – that is not a good thing. The ocean garbage floats are not huge amounts of plastic bags and bottles but instead huge amounts of small and tiny plastic particles. I know using corn based bags has been looked at previously and used.