Category Archives: Life Science

Rat Brain Cells, in a Dish, Flying a Plane

[the video was removed]

Adaptive Flight Control With Living Neuronal Networks on Microelectrode Arrays [broken link was removed] (open access paper) by Thomas B. DeMarse and Karl P. Dockendorf Department of Biomedical Engineering, University of Florida

investigating the ability of living neurons to act as a set of neuronal weights which were used to control the flight of a simulated aircraft. These weights were manipulated via high frequency stimulation inputs to produce a system in which a living neuronal network would “learn” to control an aircraft for straight and level flight.

A system was created in which a network of living rat cortical neurons were slowly adapted to control an aircraft’s flight trajectory. This was accomplished by using high frequency stimulation pulses delivered to two independent channels, one for pitch, and one for roll. This relatively simple system was able to control the pitch and roll of a simulated aircraft.

When Dr. Thomas DeMarse[broken link was removed] first puts the neurons in the dish, they look like little more than grains of sand sprinkled in water. However, individual neurons soon begin to extend microscopic lines toward each other, making connections that represent neural processes. “You see one extend a process, pull it back, extend it out — and it may do that a couple of times, just sampling who’s next to it, until over time the connectivity starts to establish itself,” he said. “(The brain is) getting its network to the point where it’s a live computation device.”

To control the simulated aircraft, the neurons first receive information from the computer about flight conditions: whether the plane is flying straight and level or is tilted to the left or to the right. The neurons then analyze the data and respond by sending signals to the plane’s controls. Those signals alter the flight path and new information is sent to the neurons, creating a feedback system.

“Initially when we hook up this brain to a flight simulator, it doesn’t know how to control the aircraft,” DeMarse said. “So you hook it up and the aircraft simply drifts randomly. And as the data come in, it slowly modifies the (neural) network so over time, the network gradually learns to fly the aircraft.”

Although the brain currently is able to control the pitch and roll of the simulated aircraft in weather conditions ranging from blue skies to stormy, hurricane-force winds, the underlying goal is a more fundamental understanding of how neurons interact as a network, DeMarse said.

Related: Neural & Hybrid Computing Laboratory @ University of Florida [broken link was removed] – UF Scientist: “Brain” In A Dish Acts As Autopilot, Living Computer [broken link was removed] – Roachbot: Cockroach Controlled Robot – New Neurons in Old Brains – posts on brain research – Viruses and What is Life – Great Self Portrait of Astronaut Engineer

Dealth of Artic Plankton a Warning on Warming

Death bloom of plankton a warning on warming by David Perlman

Vanishing Arctic sea ice brought on by climate change is causing the crucially important microscopic marine plants called phytoplankton to bloom explosively and die away as never before, a phenomenon that is likely to create havoc among migratory creatures that rely on the ocean for food, Stanford scientists have found.
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Phytoplankton throughout the world’s oceans is the crucial nutrient at the base of the food web on which all marine life depends; when it’s plentiful, life thrives and when it’s gone, marine life is impossible.
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“It’s a complex system,” Arrigo said in an interview, “but as the changes in ice cover throw the timing of phytoplankton abundance off, then the birds and animals whose brains have long been programmed to migrate north at specific times of the year will have missed the boat if there’s no nourishment for them when they get there.”

Every spring and summer, phytoplankton in the Arctic blooms richly in explosive pulses, nourished by nitrogen and phosphorous in the seawater, and when those chemicals are consumed, the blooms end, Arrigo said.

Save the Microbes, Save the World

The panel starts speaking at about minute 14. The technical presentation of the video could be better (likely will be as we develop good, easy ways to capture speaking events for web delivery) but their is some interesting content.

Single-Celled Giant Provides New Early-Evolution Perspective

Discovery of Giant Roaming Deep Sea Protist Provides New Perspective on Animal Evolution
Biologist Mikhail “Misha” Matz and his colleagues recently discovered the grape-sized protists and their complex tracks on the ocean floor near the Bahamas. DNA analysis confirmed that the giant protist found by Matz and his colleagues in the Bahamas is Gromia sphaerica, a species previously known only from the Arabian Sea.

Matz says the protists probably move by sending leg-like extensions, called pseudopodia, out of their cells in all directions. The pseudopodia then grab onto mud in one direction and the organism rolls that way, leaving a track. Hr says the giant protists’ bubble-like body design is probably one of the planet’s oldest macroscopic body designs, which may have existed for 1.8 billion years.

“I personally think now that the whole Precambrian may have been exclusively the reign of protists,” says Matz. “Our observations open up this possible way of interpreting the Precambrian fossil record.”

He says the appearance of all the animal body plans during the Cambrian explosion might not just be an artifact of the fossil record. There are likely other mechanisms that explain the burst-like origin of diverse multicellular life forms.

Single-Celled Giant Upends Early Evolution

Slowly rolling across the ocean floor, a humble single-celled creature is poised to revolutionize our understanding of how complex life evolved on Earth.

A distant relative of microscopic amoebas, the grape-sized Gromia sphaerica was discovered once before, lying motionless at the bottom of the Arabian Sea. But when Mikhail Matz of the University of Texas at Austin and a group of researchers stumbled across a group of G. sphaerica off the coast of the Bahamas, the creatures were leaving trails behind them up to 50 centimeters (20 inches) long in the mud.

The trouble is, single-celled critters aren’t supposed to be able to leave trails. The oldest fossils of animal trails, called ‘trace fossils’, date to around 580 million years ago, and paleontologists always figured they must have been made by multicellular animals with complex, symmetrical bodies.

How Bleach Kills Bacteria

Developed more than 200 years ago and found in households around the world, chlorine bleach is among the most widely used disinfectants, yet scientists never have understood exactly how the familiar product kills bacteria. In fact, Hypochlorite, the active ingredient of household bleach, attacks essential bacterial proteins, ultimately killing the bugs.

“As so often happens in science, we did not set out to address this question,” said Jakob, an associate professor of molecular, cellular and developmental biology. “But when we stumbled on the answer midway through a different project, we were all very excited.”

Jakob and her team were studying a bacterial protein known as heat shock protein 33 (Hsp33), which is classified as a molecular chaperone. The main job of chaperones is to protect proteins from unfavorable interactions, a function that’s particularly important when cells are under conditions of stress, such as the high temperatures that result from fever.

“At high temperatures, proteins begin to lose their three-dimensional molecular structure and start to clump together and form large, insoluble aggregates, just like when you boil an egg,” said lead author Jeannette Winter, who was a postdoctoral fellow in Jakob’s lab. And like eggs, which once boiled never turn liquid again, aggregated proteins usually remain insoluble, and the stressed cells eventually die.

Jakob and her research team figured out that bleach and high temperatures have very similar effects on proteins. Just like heat, the hypochlorite in bleach causes proteins to lose their structure and form large aggregates.

These findings are not only important for understanding how bleach keeps our kitchen countertops sanitary, but they may lead to insights into how we fight off bacterial infections. Our own immune cells produce significant amounts of hypochlorite as a first line of defense to kill invading microorganisms. Unfortunately, hypochlorite damages not just bacterial cells, but ours as well. It is the uncontrolled production of hypochlorite acid that is thought to cause tissue damage at sites of chronic inflammation.

How did studying the protein Hsp33 lead to the bleach discovery? The researchers learned that hypochlorite, rather than damaging Hsp33 as it does most proteins, actually revs up the molecular chaperone. When bacteria encounter the disinfectant, Hsp33 jumps into action to protect bacterial proteins against bleach-induced aggregation.

“With Hsp33, bacteria have evolved a very clever system that directly senses the insult, responds to it and increases the bacteria’s resistance to bleach,” Jakob said.

Marine Plankton From 100 Million Years Ago Found in Amber

photo of foraminifer in amber

Marine microorganisms have been found in amber dating from the middle of the Cretaceous period. The fossils were collected in Charente, in France. This completely unexpected discovery will deepen our understanding of these lost marine species as well as providing precious data about the coastal environment of Western France during the Cretaceous. This work was carried out by researchers at the GÃ©osciences Rennes laboratory, together with researchers from the PalÃ©obiodiversitÃ© et PalÃ©oenvironnement laboratory in Paris and the Centre de GÃ©ochimie de la Surface in Strasbourg.

Amber is a fossil resin with a reputation for preserving even the most minute details of insects and other terrestrial arthropods (spiders, scorpions, mites) that lived in resiniferous trees. The forest-based provenance of amber in theory makes it impossible for marine animals to be trapped in the resin. Nonetheless, researchers from the GÃ©osciences Rennes laboratory have discovered various inclusions of marine plankton in amber from the Mid-Cretaceous (100 to 98 million years ago). These micro-organisms are found in just a few pieces of amber among the thousands that have been studied, but show a remarkable diversity: unicellular algae, mainly diatoms found in large numbers, traces of animal plankton, such as radiolaria and a foraminifer, spiny skeletons of sponges and of echinoderms.

Foraminifera (the photo shows one in Amber) are amoeboid protists with reticulating pseudopods, fine strands of cytoplasm that branch and merge to form a dynamic net.[1] They typically produce a test, or shell, which can have either one or multiple chambers, some becoming quite elaborate in structure.[2] These shells are made of calcium carbonate (CaCO3) or agglutinated sediment particles. About 275,000 species are recognized, both living and fossil.[citation needed] They are usually less than 1 mm in size.”

Carried out together with researchers at the MusÃ©um national d’histoire naturelle, the study of diatoms pushed back by 10 to 30 million years the known date for the appearance of certain marine forms of this type of algae. This new information, taken together with recent data on molecular phylogeny, marks a huge advance in our understanding of the complex evolutionary history of diatoms.

The presence of these marine organisms in the amber is an ecological paradox. How did these marine species become stuck and then trapped in the conifers’ resin? The most likely scenario is that the forest producing the amber was very close to the coast, potentially shrouded by plankton-bearing mist or flooded by sea water during storms.

The preservation of marine organisms in amber is an exceptional asset, allowing us to deepen our understanding of these lost species and to have a clear idea about the coastal environment of Western France during the Cretaceous.

press release

Bacteria and Efficient Food Digestion

Gut Bacteria May Cause And Fight Disease, Obesity

“We’re all sterile until we’re born,” says Glenn Gibson, a microbiologist at the University of Reading in Britain. “We haven’t got anything in us right up until the time we come into this big, bad, dirty world.”

But as soon as we pass out of the birth canal, when we are fetched by a doctor’s hands, placed in a hospital crib, put on our mother’s breast, when we drag a thumb across a blanket and stick that thumb in our mouths, when we swallow our first soft food, we are invaded by all sorts of bacteria. Once inside, they multiply – until the bacteria inside us outnumber our human cells.
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University of Chicago immunologist Alexander Chervonsky, with collaborators from Yale University, recently reported that doses of the right stomach bacteria can stop the development of type 1 diabetes in lab mice. “By changing who is living in our guts, we can prevent type 1 diabetes,” he told The Wall Street Journal.

The bottom line: We now have two sets of genes to think about – the ones we got from our parents and the ones of organisms living inside us. Our parents’ genes we can’t change, but the other set? Now that is one of the newest and most exciting fields in cell biology.

Follow link with related podcast: Gut bacteria may cause and fight, disease, obesity. This whole area of the ecosystem within us and our health I find fascinating. And I fall for confirmation bias on things like becoming inefficient at converting food to energy as a way reduce obesity.

You could have two people sitting down to a bowl of cheerios, they could each eat the same number of cheerios but because of a difference in their gut bacteria one will get more calories than the other.

They then gave an example of the difference being 95 calories versus 99 calories. Hardly seems huge but it would add up. Still that is a less amazing difference than I was expecting.

Friday Fun: Octopus Juggling Fellow Aquarium Occupants

photo of Otto the Octopus

Otto the octopus wreaks havoc

Otto is constantly craving for attention and always comes up with new stunts so we have realised we will have to keep more careful eye on him – and also perhaps give him a few more toys to play with.

“Once we saw him juggling the hermit crabs in his tank, another time he threw stones against the glass damaging it. And from time to time he completely re-arranges his tank to make it suit his own taste better – much to the distress of his fellow tank inhabitants.”

Staff believe that the octopus called Otto had been annoyed by the bright light shining into his aquarium and had discovered he could extinguish it by climbing onto the rim of his tank and squirting a jet of water in its direction. The short-circuit had baffled electricians as well as staff at the Sea Star Aquarium in Coburg, Germany, who decided to take shifts sleeping on the floor to find out what caused the mysterious blackouts.

Copper Doorknobs and Faucets Kill 95% of Superbugs

Copper door handles and taps kill 95% of superbugs in hospitals

A study found that copper fittings rapidly killed bugs on hospital wards, succeeding where other infection control measures failed.
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It is thought the metal ‘suffocates’ germs, preventing them breathing. It may also stop them from feeding and destroy their DNA. Lab tests show that the metal kills off the deadly MRSA and C difficile superbugs. It also kills other dangerous germs, including the flu virus and the E coli food poisoning bug.
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Researcher Professor Peter Lambert, of Aston University, Birmingham, said: ‘The numbers decreased always on copper but not on the steel surfaces.’
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The healing power of copper has been recognised for thousands of years. More than 4,000 years ago, the Egyptians used it to sterilise wounds and drinking water and the Aztecs treated skin conditions with the metal. The ancient Greeks also knew of its benefits. Hippocrates, sometimes called ‘the father of medicine’, noted that it could be used to treat leg ulcers.

Vampire Moth Discovered

Entomologist Jennifer Zaspel at the University of Florida in Gainesville said the discovery suggests the moth population could be on an “evolutionary trajectory” away from other C. thalictri populations.

In January, she will compare the Russian population’s DNA to that of other populations and other species to confirm her suspicions. “Based on geography, based on behavior, and based on a phenotypic variation we saw in the wing pattern, we can speculate that this represents something different, something new,” Zaspel said.
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Only male moths exhibit blood feeding, she noted, raising the possibility that as in some species of butterflies and other moths, the Russian moths do it to pass on salt to females during copulation.

“There is no evidence it prolongs the life of the male, or anything like that,” she said. “So we suspect that it is probably going to the female.” The sexual gift, she said, would provide a nutritional boost to young larvae that feed on leaf-rich, but sodium-poor, diets.