Category Archives: Research

Waste Treatment Plants Result in Super Bacteria

Multiple antibiotic-resistant bacteria has emerged as one of the top public health issues worldwide in the last few decades as the overuse of antibiotics and other factors have caused bacteria to become resistant to common drugs. Chuanwu Xi‘s group chose to study Acinetobacter because it is a growing cause of hospital-acquired infections and because of its ability to acquire antibiotic resistance.

Xi said the problem isn’t that treatment plants don’t do a good job of cleaning the water—it’s that they simply aren’t equipped to remove all antibiotics and other pharmaceuticals entering the treatment plants.

The treatment process is fertile ground for the creation of superbugs because it encourages bacteria to grow and break down the organic matter. However, the good bacteria grow and replicate along with the bad. In the confined space, bacteria share resistant genetic materials, and remaining antibiotics and other stressors may select multi-drug resistant bacteria.

While scientists learn more about so-called superbugs, patients can do their part by not insisting on antibiotics for ailments that antibiotics don’t treat, such as a common cold or the flu, Xi said. Also, instead of flushing unused drugs, they should be saved and disposed of at designated collection sites so they don’t enter the sewer system.

The next step, said Xi, is to see how far downstream the superbugs survive and try to understand the link between aquatic and human superbugs. This study did not look past 100 yards.

Xi’s colleagues include visiting scholar Yongli Zhang; Carl Marrs, associate professor of public health; and Carl Simon, professor of mathematics.

Xi and colleagues found that while the total number of bacteria left in the final discharge effluent declined dramatically after treatment, the remaining bacteria was significantly more likely to resist multiple antibiotics than bacteria in water samples upstream. Some strains resisted as many as seven of eight antibiotics tested. The bacteria in samples taken 100 yards downstream also were more likely to resist multiple drugs than bacteria upstream.

Full press release

The Great Sunflower Project

photo of sunflower (Helianthus Annuus Taiyo)

Sunflower photo from WikiMedia – Helianthus Annuus ‘Taiyo’

The Great Sunflower Project provides a way for you to engage in the ongoing study of bees and colony collapse disorder. The study uses the annual Lemon Queen sunflowers (Helianthus annuus), that can be grown in a pot on a deck or patio or in a garden (and they will send you seeds).

How do bees make fruits and vegetables?

Bees help flowers make seeds and fruits. Bees go to flowers in your garden to find pollen (the powder on the flower) and nectar which is a sweet liquid. Flowers are really just big signs advertising to bees that there is pollen or nectar available – though sometimes a flower will cheat and have nothing! The markings on a flower guide the bee right into where the pollen or nectar is.

All flowers have pollen. Bees gather pollen to feed their babies which start as eggs and then grow into larvae. It’s the larvae that eat the pollen. Bees use the nectar for energy. When a bee goes to a flower in your garden to get nectar or pollen, they usually pick up pollen from the male part of the flower which is called an anther. When they travel to the next flower looking for food, they move some of that pollen to the female part of the next plant which is called a stigma. Most flowers need pollen to make seeds and fruits.

After landing on the female part, the stigma, the pollen grows down the stigma until it finds an unfertilized seed which is called an ovary. Inside the ovary, a cell from the pollen joins up with cells from the ovary and a seed is born! For many of our garden plants, the only way for them to start a new plant is by growing from a seed Fruits are just the parts of the plants that have the seeds. Some fruits are what we think of as fruits when we are in the grocery store like apples and oranges. Other fruits are vegetables like tomatoes and cucumbers and peppers.

Sun Missing It’s Spots

Image courtesy of SOHO, shows an image of the sun on July 19th 2000 and March 18th 2009.

Sun Oddly Quiet

The sun is the least active it’s been in decades and the dimmest in a hundred years. The lull is causing some scientists to recall the Little Ice Age, an unusual cold spell in Europe and North America, which lasted from about 1300 to 1850. The coldest period of the Little Ice Age, between 1645 and 1715, has been linked to a deep dip in solar storms known as the Maunder Minimum.
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Sunspots, which can be visible without a telescope, are dark regions that indicate intense magnetic activity on the sun’s surface. Such solar storms send bursts of charged particles hurtling toward Earth that can spark auroras, disrupt satellites, and even knock out electrical grids.

Graphene: Engineered Carbon

A material for all seasons

Graphene, a form of the element carbon that is just a single atom thick, had been identified as a theoretical possibility as early as 1947.
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Its unique electrical characteristics could make graphene the successor to silicon in a whole new generation of microchips, surmounting basic physical constraints limiting the further development of ever-smaller, ever-faster silicon chips.

But that’s only one of the material’s potential applications. Because of its single-atom thickness, pure graphene is transparent, and can be used to make transparent electrodes for light-based applications such as light-emitting diodes (LEDs) or improved solar cells.
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Graphene could also substitute for copper to make the electrical connections between computer chips and other electronic devices, providing much lower resistance and thus generating less heat. And it also has potential uses in quantum-based electronic devices that could enable a new generation of computation and processing.

“The field is really in its infancy,” says Michael Strano, associate professor of chemical engineering who has been investigating the chemical properties of graphene. “I don’t think there’s any other material like this.”

The mobility of electrons in graphene — a measure of how easily electrons can flow within it — is by far the highest of any known material. So is its strength, which is, pound for pound, 200 times that of steel. Yet like its cousin diamond, it is a remarkably simple material, composed of nothing but carbon atoms arranged in a simple, regular pattern.

“It’s the most extreme material you can think of,” says Palacios. “For many years, people thought it was an impossible material that couldn’t exist in nature, but people have been studying it from a theoretical point of view for more than 60 years.”

Merck and Elsevier Publish Phony Peer-Review Journal

Elsevier is one of those publishers fighting open science. They try to claim that the government publishing government funded research in an open way will tarnish science. The argument makes no sense to me. Here is another crazy action on their part: they published a “journal” funded by Merck to promote Merck products. Merck Makes Phony Peer-Review Journal:

Merck cooked up a phony, but real sounding, peer reviewed journal and published favorably looking data for its products in them. Merck paid Elsevier to publish such a tome, which neither appears in MEDLINE or has a website, according to The Scientist.
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What’s sad is that I’m sure many a primary care physician was given literature from Merck that said, “As published in Australasian Journal of Bone and Joint Medicine, Fosamax outperforms all other medications….” Said doctor, or even the average researcher wouldn’t know that the journal is bogus. In fact, knowing that the journal is published by Elsevier gives it credibility!

As I have said the journals fighting open science should have their credibility questioned. They are putting their outdated business model above science. We should not see organizations that are focused on closing science research through deceptive publicity efforts and lobbying efforts as credible.

Swine Flu: a Quick Overview

World Health Organization on Swine influenza

After reviewing available data on the current situation, Committee members identified a number of gaps in knowledge about the clinical features, epidemiology, and virology of reported cases and the appropriate responses. The Committee advised that answers to several specific questions were needed to facilitate its work.

The Committee nevertheless agreed that the current situation constitutes a public health emergency of international concern.

Based on this advice, the Director-General has determined that the current events constitute a public health emergency of international concern, under the Regulations.

Swine flu: a quick overview–and new New York and Kansas cases by Tara Smith

while the cases in the US have been mild and no deaths have occurred that we’re aware of, it seems in Mexico that young people are dying from this–a group that is typically not hard-hit by seasonal influenza viruses. Readers familiar with influenza and know the history of the 1918 influenza pandemic will recall that the “young and healthy” were disproportionally struck by that virus as well–so this knowledge is currently disconcerting and worrisome, but there are so many gaps in our information as far as what’s really going on in Mexico that it’s difficult to make heads or tails out of this data right now.

Third, is this really a new virus? So few influenza isolates are actually analyzed each year (in proportion to the number of people infected) that we aren’t sure yet whether this is something brand-new, or something that has been circulating at a low level for awhile, but just hadn’t been picked up. After all, H1N1 is a common serotype, so additional molecular testing is needed to determine that it’s “swine flu” versus “human” H1N1.
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this is a fast-developing story, and it will take much more investigation and field work to determine the true extent of the virus’s spread in the population; to figure out… how efficiently it’s transmitted…

This is very early in the scientific inquiry process looking into what exactly is going on. It is too early to tell how serious a threat this is. The reaction of WHO, CDC though shows they are taking the threat seriously. By far the biggest danger in such situations, is reacting too slowly to serious and contagious threats. If you wait to react until proof exists that the situation is very serious the situation can be almost impossible to control. So you need to react quickly to shut down the spread of the threat, hopefully before it has spread too far.

Evolutionary Robotics

Evolutionary Robotics, chapter of Handbook of Robotics, is interesting and includes a good explanation of the difference between evolution and learning:

Evolution and learning (or phylogenetic and ontogenetic
adaptation) are two forms of biological adaptation that differ in space and time. Evolution is a process of selective reproduction and substitution based on the existence of a population of individuals displaying variability at the genetic level. Learning, instead, is a set of modifications taking place within each single individual during its own life time.

Evolution and learning operate on different time scales. Evolution is a form of adaptation capable of capturing relatively slow environmental changes that

might encompass several generations (e.g., the perceptual characteristics of food sources for a given species). Learning, instead, allows an individual to adapt to environmental modifications that are unpredictable at the generational level. Learning might include a variety of mechanisms that produce adaptive changes in an individual during its lifetime, such as physical development, neural maturation, variation of the connectivity between neurons, and synaptic plasticity. Finally, whereas evolution operates on the genotype, learning affects only the phenotype and phenotypic modifications cannot directly modify the genotype.
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Recent research showed that teams of evolved robots can: (a) develop robust and effective behavior, (b) display an ability to differentiate their behavior so
to better cooperate; (c) develop communication capabilities and a shared communication system.

Iron-breathing Species Isolated in Antarctic for Millions of Years

Graphic showing environment of Antarctic subglacial microbes

Graphic of Blood Falls showing microbial community environment in the Antarctic by Zina Deretsky at NSF)

A reservoir of briny liquid buried deep beneath an Antarctic glacier supports hardy microbes that have lived in isolation for millions of years, researchers report this week. The discovery of life in a place where cold, darkness, and lack of oxygen would previously have led scientists to believe nothing could survive comes from a team led by researchers at Harvard University and Dartmouth College.

Despite their profound isolation, the microbes are remarkably similar to species found in modern marine environments, suggesting that the organisms now under the glacier are the remnants of a larger population that once occupied an open fjord or sea.

“It’s a bit like finding a forest that nobody has seen for 1.5 million years,” says Ann Pearson, Thomas D. Cabot Associate Professor of Earth and Planetary Sciences in Harvard’s Faculty of Arts and Sciences. “Intriguingly, the species living there are similar to contemporary organisms, and yet quite different — a result, no doubt, of having lived in such an inhospitable environment for so long.”

“This briny pond is a unique sort of time capsule from a period in Earth’s history,” says lead author Jill Mikucki, now a research associate in the Department of Earth Sciences at Dartmouth and visiting fellow at Dartmouth’s Dickey Center for International Understanding and its Institute of Arctic Studies. “I don’t know of any other environment quite like this on Earth.”

Chemical analysis of effluent from the inaccessible subglacial pool suggests that its inhabitants have eked out a living by breathing iron leached from bedrock with the help of a sulfur catalyst. Lacking any light to support photosynthesis, the microbes have presumably survived by feeding on the organic matter trapped with them when the massive Taylor Glacier sealed off their habitat an estimated 1.5 to 2 million years ago.
Continue reading →

Artificial Intelligence Finds Ancient Indus Script Matches Spoken Language

Artificial Intelligence Cracks 4,000-Year-Old Mystery by Brandon Keim

An ancient script that’s defied generations of archaeologists has yielded some of its secrets to artificially intelligent computers.
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The Indus script, used between 2,600 and 1,900 B.C. in what is now eastern Pakistan and northwest India, belonged to a civilization as sophisticated as its Mesopotamian and Egyptian contemporaries. However, it left fewer linguistic remains. Archaeologists have uncovered about 1,500 unique inscriptions from fragments of pottery, tablets and seals. The longest inscription is just 27 signs long.
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They fed the program sequences of four spoken languages: ancient Sumerian, Sanskrit and Old Tamil, as well as modern English. Then they gave it samples of four non-spoken communication systems: human DNA, Fortran, bacterial protein sequences and an artificial language.

The program calculated the level of order present in each language. Non-spoken languages were either highly ordered, with symbols and structures following each other in unvarying ways, or utterly chaotic. Spoken languages fell in the middle.

When they seeded the program with fragments of Indus script, it returned with grammatical rules based on patterns of symbol arrangement. These proved to be moderately ordered, just like spoken languages.

Nanoparticles With Scorpion Venom Slow Cancer Spread

In a, chlorotoxin molecules, colored blue and green, attach themselves to a central nanoparticle. In b, each nanoprobe offers many chlorotoxin molecules that can simultaneously latch on to many MMP-2s, depicted here in yellow, which are thought to help tumor cells travel through the body. In c, over time nanoprobes draw more and more of the MMP-2 surface proteins into the cell, slowing the tumor’s spread. Image from the University of Washington.

University of Washington researchers found they could cut the spread of cancerous cells by 98 percent, compared to 45 percent for the scorpion venom alone, by combining nanoparticles with a scorpion venom compound already being investigated for treating brain cancer.

For more than a decade scientists have looked at using chlorotoxin, a small peptide isolated from scorpion venom, to target and treat cancer cells. Chlorotoxin binds to a surface protein overexpressed by many types of tumors, including brain cancer. Previous research by Miqin Zhang‘s group combined chlorotoxin with nanometer-scale particles of iron oxide, which fluoresce at that size, for both magnetic resonance and optical imaging.

Chlorotoxin also disrupts the spread of invasive tumors — specifically, it slows cell invasion, the ability of the cancerous cell to penetrate the protective matrix surrounding the cell and travel to a different area of the body to start a new cancer. The MMP-2 on the cell’s surface, which is the binding site for chlorotoxin, is hyperactive in highly invasive tumors such as brain cancer. Researchers believe MMP-2 helps the cancerous cell break through the protective matrix to invade new regions of the body. But when chlorotoxin binds to MMP-2, both get drawn into the cancerous cell.

Research showed that the cells containing nanoparticles plus chlorotoxin were unable to elongate, whereas cells containing only nanoparticles or only chlorotoxin could stretch out. This suggests that the nanoparticle-plus-chlorotoxin disabled the machinery on the cell’s surface that allows cells to change shape, yet another step required for a tumor cell to slip through the body.

So far most cancer research has combined nanoparticles either with chemotherapy that kills cancer cells, or therapy seeking to disrupt the genetic activity of a cancerous cell. This is the first time that nanoparticles have been combined with a therapy that physically stops cancer’s spread.

Full press release