Category Archives: Life Science

Cool Crow Research

photo of crow vending machine

Very cool project – A Vending Machine for Crows

The goal of this project is to create a device that will autonomously train crows. Initially we’re training them to deposit dropped coins they find on the ground in exchange for peanuts, but eventually we hope to be able to train them to search and rescue, or to collect garbage, or who knows!
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This is the highest-risk segment of the machine’s operation. At this point coins alone are made available whenever the bird lands on the perch. However, should a bird peck or sweep coins off the tray and cause a coin to fall down the funnel, the device then produces some peanuts. This stage is designed to cement in the crows’ mind the relationship between coins going down the funnel and peanuts being made available.
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Finally we shift the device into its intended, and long-term state of only providing peanuts when coins go down the funnel. Nothing is otherwise provided aside from coins scattered around the device at the beginning of the project.

Joshua Klein Thesis presentation definitely watch this! (the webcast takes like 30 seconds before the talk starts – it is worth the wait). Watch a video from the University of Ithaca site (with Dr. Kevin McGowan).

Other sites that also are mentioned as possible sites: Dr. Anne Clark, University of Binghamton (with a captive population of crows); Dr. Natalie Jeremijenko (seed podcast), Dr. Carolee Caffrey, Harvard and Dr. James Ha, University of Washington. Read the Paper by Joshua Klein about the plans for the experiment.

Disrupting Bacteria Communication

Princeton scientists break cholera’s lines of communication

A team of Princeton scientists has discovered a key mechanism in how bacteria communicate with each other, a pivotal breakthrough that could lead to treatments for cholera and other bacterial diseases.

The mechanism is a chemical that cholera bacteria use for transmitting messages to each other, known as CAI-1, and has been isolated in the lab of molecular biologist Bonnie Bassler. Her team has shown that the chemical also can be used to disrupt the communication that exists among the bacteria, potentially halting the disease’s progress. The discovery could lead to an entirely new class of antibiotics.
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Higgins isolated the CAI-1 chemical, which occurs naturally in cholera. Then, Megan Pomianek, a graduate student in the laboratory of Martin Semmelhack, a professor of chemistry at Princeton, determined how to make the molecule in the laboratory. Higgins used this chemical essentially to control cholera’s behavior in lab tests.

The team found that when CAI-1 is absent, cholera bacteria act as pathogens. But when the bacteria detect enough of this chemical, they stop making biofilms and releasing toxins, perceiving that it is time to leave the body instead. “Our findings demonstrate that if you supply CAI-1 to cholera, you can flip their switches to stop the attack,” Higgins said.

Chemist Helen Blackwell of the University of Wisconsin-Madison praised the study, calling it a breakthrough for quorum sensing research, and possibly for medical science.

The Brain is Wired to Mull Over Decisions

New studies have identified a specific neural circuit in the brains of monkeys that is activated when they postpone acting on a decision. The circuit is thought to keep potential choices brewing in memory even after a decision has already been made.

The brain may continue to consider the options even after a decision is made because that extra consideration may sometimes result in a change of mind – and a possible reward, such as a tastier meal. The researchers said that their findings could offer important insight into the function of neural circuits that drive the brain’s memory and decision-making machinery.
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the researchers conducted experiments in which they required the monkeys to delay their decision. At the same time, the researchers recorded the electrical activity of neurons in a region called the medial premotor cortex—one of the brain regions involved in decision-making and motor choice.

“To our surprise, when the monkeys held the decision for several seconds, what we saw in the activity of these brain cells in the medial premotor cortex is that they were still remembering the sensory information on which the decision was based,” said Romo. “During that time the neurons were recalling the first stimulus, recalling the second, comparing the second against the first, and even reporting in their activity the categorical decision.”

Remove the Identical Stretches of DNA Found in Mice, Rats, and Humans and What Happens?

A Real Genetic Headscratcher by Derek Lowe:

As you root through genomic sequences – and there are more and more of them to root through these days – you come across some stretches of DNA that hardly seem to vary at all. The hard-core “ultraconserved” parts, first identified in 2004, are absolutely identical between mice, rats, and humans.
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Even important enzyme sequences vary a bit among the three species, so what could these pristine stretches (some of which are hundreds of base pairs long) be used for? The assumption, naturally, has been that whatever it is, it must be mighty important, but if we’re going to be scientists, we can’t just go around assuming that what we think must be right. A team at Lawrence Berkeley and the DOE put things to the test recently by identifying four of the ultraconserved elements that all seem to be located next to critical genes – and deleting them.

The knockout mice turned out to do something very surprising indeed. They were born normally, but then they grew up normally. When they reached adulthood, though, they were completely normal. Exhaustive biochemical and behavioral tests finally uncovered the truth: they’re basically indistinguishable from the wild type. Hey, I told you it was surprising. This must have been the last thing that the researchers expected.

What a great example of scientists at work. It will be interesting to see where this goes.

MRSA Blows Up Defender Cells

Superbug succeeds by blowing up defender cells, scientists learn

While only 14 percent of serious MRSA infections are the community associated kind, they have drawn attention in recent months with a spate of reports in schools, including the death of a 17-year-old Virginia high school student. Both hospital-associated and community-associated MRSA contained genes for the peptides. But their production was much higher in the CA-MRSA, the researchers said.
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The compounds first cause inflammation, drawing the immune cells to the site of the infection, and then destroy those cells. The research was conducted in mice and with human blood in laboratory tests. Within five minutes of exposure to the peptides from CA-MRSA, human neutrophils showed flattening and signs of damage to their membrane, researchers said. After 60 minutes, many cells had disintegrated completely.

“This elegant work helps reveal the complex strategy that S. aureus has developed to evade our normal immune defenses,” Dr. Anthony S. Fauci, NIAID director, said in a statement. “Understanding what makes the infections caused by these new strains so severe and developing new drugs to treat them are urgent public health priorities.”

Fish Discovery: Breathes Air for Months at a Time

Fish Lives in Logs, Breathing Air, for Months at a Time:

A tiny Western Atlantic fish does something never before seen: It makes like a bird, living in mangrove wood for months at a time. A team of U.S. and English scientists accidentally discovered the unique behavior, which they call “logpacking,” during recent excursions to Belize and Florida. They were studying how the mangrove rivulus—an animal already infamous for its bizarre sexual behavior—survived the frequent dry spells that strike its swampy forest habitat.

“One of us kicked at a log, which broke apart and out came the fish!” said team leader Scott Taylor of Brevard County, Florida’s Environmentally Endangered Lands Program. The mangrove rivulus, also known as the mangrove killifish, is native to the Americas and is about two inches (five centimeters) long. The fish has long been studied for its many unique features.

It’s the only vertebrate known to naturally self-fertilize, for example. In some populations, it can become a hermaphrodite, developing both male and female parts simultaneously, to produce clones of itself. The animal can also live out of water for up to 66 days, Taylor said, and is one of very few fish species that spend their entire lives in mangrove swamps. Most fish move in and out of the areas as water sources dwindle.

New and Old Ways to Make Flu Vaccines

New and Old Ways to Make Flu Vaccines by Nell Greenfieldboyce, NPR:

Standard Practice
Pros: Millions of Americans receive this [standard] vaccine every year. It’s safe and well tolerated. Its production begins in hens’ eggs — a tried and true technology for 50 years.
Cons: Eggs must be ordered many months in advance, and millions of doses require millions of eggs.

Live-Attenuated Vaccine
Pros: This newer method of production results in a vaccine that has a flu virus that is crippled, so it can’t cause disease. But the virus is not killed, as is the case in the standard vaccine. The vaccine also can be given as a nasal spray.
Cons: More expensive than standard vaccine, and also produced in eggs. Not approved for young children or older people.

Cell-Based Vaccine
Pros: This vaccine can be produced in giant vats of living cells. Such a production method means it can be scaled up much faster than egg-based vaccines, making it more useful in a pandemic. Several versions have been tested successfully in people.
Cons: Won’t be widely available for a few years. Clinical trials are under way, but no flu vaccine made this way is currently approved by the Food and Drug Administration.

Cat Joins Exclusive Genome Club

Cat joins exclusive genome club

The domestic cat now joins the select club of mammals whose genome has been deciphered – including dogs, chimps, rats, mice, cows and people. The genome map is expected to shed light on both feline and human disease. Cats get hundreds of illnesses similar to human ones, including a feline version of HIV, known as FIV, and a hereditary form of blindness.
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Cats are among the 26 mammals chosen by the National Human Genome Research Institute in the US for less complete or “light” genome sequencing. Scientists use the so-called “shot-gun” sequencing method, where DNA is extracted, chopped into pieces, sequenced, and then pieced back together again.

It has yielded a rough version of the cat genome, including around 60% of Cinnamon’s DNA “letters” with many gaps in between. A more complete version, expected next year, will be used to make more detailed comparisons with other animals.

The Study of Bee Colony Collapses Continues

The attempts to discover the causes of the die off of bees in the USA continues. This effort provides a good example of the difficulty of learning what really happens around us. Often, once things are worked out, and explained they seem simple and even obvious. But while trying to figure events taking place (like the bee colony collapses), scientists have significant challenges. The hard work and the application of scientific concepts by scientists allow us to learn and adapt. I think the difficulty can paint a valuable picture of what science is about. That search for understanding is wonderful to see and something fundamental to the human experience. Disappearing Bee Mystery Deepens

One year ago, beekeepers across the country began to report that worker bees were inexplicably abandoning their hives and leaving the brood to die. Although firm statistics are hard to come by, so-called colony collapse disorder may have afflicted as many as 25% of U.S. beekeepers and perhaps others around the world. Possible culprits included pesticides, parasites, and chronic stress from poor nutrition and the long-distance truck rides that many commercial hives undergo.
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For that matter, no one has yet shown that IAPV can cause colonies to collapse. “Until you have introduced the virus and caused disease, you’re just postulating,” cautions Bruce Webb, an entomologist at the University of Kentucky in Lexington. “The conclusive data are not in.”

Plumpynut – Food Savior

A Life Saver Called “Plumpynut”

Every year, malnutrition kills five million children — that’s one child every six seconds. But now, the Nobel Prize-winning relief group “Doctors Without Borders” says it finally has something that can save millions of these children. It’s cheap, easy to make and even easier to use. What is this miraculous cure? As CNN’s Anderson Cooper reports, it’s a ready-to-eat, vitamin-enriched concoction called “Plumpynut,” an unusual name for a food that may just be the most important advance ever to cure and prevent malnutrition.

“It’s a revolution in nutritional affairs,” says Dr. Milton Tectonidis, the chief nutritionist for Doctors Without Borders. “Now we have something. It is like an essential medicine. In three weeks, we can cure a kid that is looked like they’re half dead. We can cure them just like an antibiotic. It’s just, boom! It’s a spectacular response,” Dr. Tectonidis says.
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Plumpynut is a remarkably simple concoction: it is basically made of peanut butter, powdered milk, powdered sugar, and enriched with vitamins and minerals. It tastes like a peanut butter paste. It is very sweet, and because of that kids cannot get enough of it. The formula was developed by a nutritionist. It doesn’t need refrigeration, water, or cooking; mothers simply squeeze out the paste. Many children can even feed themselves. Each serving is the equivalent of a glass of milk and a multivitamin.