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Curious Cat Science and Egineering blog full tag cloud
Harvard researchers gain new insight into aging
Scientists have long known that aging causes gene expression to change, and DNA damage to accumulate. But now, research led by Harvard Medical School scientists explains the connection between the two processes in mammals.
The paper, published in the journal Cell, found that a multi-tasking protein called SIRT1 that normally acts as guardian of the genome gets dragged away to DNA fix-it jobs. When the protein abandons its normal post to work as a genetic handyman, order unravels elsewhere in the cell. Genes that are normally under its careful watch begin to flip on.
“What this paper actually implies is that aspects of aging may be reversible,” said David Sinclair, a Harvard Medical School biologist who led the research. “It sounds crazy, but in principle it should be possible to restore the youthful set of genes, the patterns that are on and off.”
The study is just the latest to draw yet more attention to sirtuins, proteins involved in the aging process
Aging is fascinating. By and large people just accept it. We see it happen to those all around us, without exception. But what causes biological aging? It is an interesting area of research.
Related: lobsters show no apparent signs of aging - Our Genome Changes as We Age - Millennials in our Lifetime? - Radical Life Extension - posts on cells
| Adaptive Flight Control With Living Neuronal Networks on Microelectrode Arrays (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 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 - UF Scientist: “Brain” In A Dish Acts As Autopilot, Living Computer - Roachbot: Cockroach Controlled Robot - New Neurons in Old Brains - posts on brain research - Viruses and What is Life - Great Self Portrait of Astronaut Engineer
The broken window theory is that as the visible deterioration of an area (broken windows, graffiti, lettering…) takes place, crime will increase. And that this starts a cycle of decline for the area feeds upon itself (a negatively reinforcing loop in system thinking parlance). The theory was put forth in an article in The Atlantic in 1982 by George L. Kelling and James Q. Wilson.
Criminology Can the can, The Economist
The researchers’ conclusion is that one example of disorder, like graffiti or littering, can indeed encourage another, like stealing. Dr Kelling was right. The message for policymakers and police officers is that clearing up graffiti or littering promptly could help fight the spread of crime.
Related: A Crack in the Broken-Windows Theory - Broken Windows Turns 25 - Reconsidering the ‘Broken Windows’ Theory - Credit Freeze Stops Identity Theft Cold
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
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.
Related: Lancelet Genome Provides Answers on Evolution - MicroRNAs Emerged Early in Evolution - Fossils of Sea Monster - Sea Urchin Genome
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.
Related: University of Michigan Press release - How do antibiotics kill bacteria? - NPR podcast on the story - Why ‘Licking Your Wounds’ Works - Researchers Learn What Sparks Plant Growth
Golf secret not all in the wrists
Surprisingly, the wrists don’t play a critical role in the swing’s outcome, according to the new model. The analysis also shows that while bigger golfers might hit further, it’s not by much. Any golfer will tell you that the idea of swinging harder to hit farther is not as straightforward as it might seem; the new results indicate that how - and when - the power develops is the key to distance.
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Prof Sharp used a computer model first to fit to the swing styles of three professionals whose swings were measured with high-speed photography in 1968: Bernard Hunt, Geoffrey Hunt and Guy Wolstenholme.
The model showed that the club-head speed, and thus drive distance, of these professionals could have been improved by increasing the torque quickly to the maximum value and maintaining it throughout the rest of the swing. It’s a delicate balance, however, and Sunday duffers may find it hard to implement Prof Sharp’s prescription.
The application of science to sports is an interesting area. Previous posts: Science of the High Jump - Sports Engineering @ MIT - Physicist Swimming Revolution - Baseball Pitch Designed in the Lab
Scientists Come Closer to Unlocking Secrets of Common Cold
Instead, the ubiquitous virus alters the activity of genes in the body, which then results in the misery that afflicts most people every year or so, according to a study in the first November issue of the American Journal of Respiratory and Critical Care Medicine.
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Human rhinovirus (HRV) causes some 30 percent to 50 percent of common colds and can also worsen more serious conditions, such as asthma.
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A “microarray analysis” of DNA showed no genetic changes eight hours after infection. But, after two days, about 6,500 genes had been affected, either with heightened activity or dampened activity.
The genes most affected by the presence of the virus were ones that make antiviral proteins and pro-inflammatory chemicals that contribute to airway inflammation, the researchers said.
Read: Learning How Viruses Evade the Immune System - Gene Carnival - Black Raspberries Alter Hundreds of Genes Slowing Cancer - Study Finds No Measurable Benefit to Flu Shots
A single molecule in the intestinal wall, activated by the waste products from gut bacteria, plays a large role in controlling whether the host animals are lean or fatty, a research team, including scientists from UT Southwestern Medical Center, has found in a mouse study.
When activated, the molecule slows the movement of food through the intestine, allowing the animal to absorb more nutrients and thus gain weight. Without this signal, the animals weigh less.
The study shows that the host can use bacterial byproducts not only as a source of nutrients, but also as chemical signals to regulate body functions. It also points the way to a potential method of controlling weight, the researchers said.
“It’s quite possible that blocking this receptor molecule in the intestine might fight a certain kind of obesity by blocking absorption of energy from the gut,” said Dr. Masashi Yanagisawa, professor of molecular genetics at UT Southwestern and a senior co-author of the study, Proceedings of the National Academy of Sciences, open access: Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41.
Humans, like other animals, have a large and varied population of beneficial bacteria that live in the intestines. The bacteria break up large molecules that the host cannot digest. The host in turn absorbs many of the resulting small molecules for energy and nutrients.
In the Big Fat Lie I mentioned some related ideas:
This research seems to be looking for a similar way to attack the obesity epidemic: reduce the efficiency of our bodies converting potential energy in the food we eat to energy we use or store. If we can make that part of the solution that will be nice. So far the reduction in our activity and increase in food intake have not been getting good results. And efforts to increase (from our current low levels) activity and reduce food intake have not been very effective.
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When under attack, plants can signal microbial friends for help
However, the infected plants whose roots had been inoculated with the beneficial microbe Bacillus subtilis were perfectly healthy. Farmers often add B. subtilis to the soil to boost plant immunity. It forms a protective biofilm around plant roots and also has antimicrobial properties, according to Bais.
Using molecular biological tools, the scientists detected the transmission of a long-distance signal, a “call for help,” from the leaves to the roots in the plants that had Bacillus in the soil. The roots responded by secreting a carbon-rich chemical–malic acid.
All plants biosynthesize malic acid, Bais explains, but only under specific conditions and for a specific purpose–in this case, the chemical was actively secreted to attract Bacillus. Magnified images of the roots and leaves showed the ratcheted-up defense response provided by the beneficial microorganisms.
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“Plants can’t move from where they are, so the only way they can accrue good neighbors is through chemistry,” Bais notes.
Related: Researchers Learn What Sparks Plant Growth - Secret Life of Microbes - Symbiotic relationship between ants and bacteria - Bacterium Living with High Level Radiation
High-School Social Skills Predict Better Earnings than Test Scores
Ten years after graduation, high-school students who had been rated as conscientious and cooperative by their teachers were earning more than classmates who had similar test scores but fewer social skills, said a new University of Illinois study.
The study’s findings challenge the idea that racial, ethnic, and socioeconomic gaps in educational attainment and earnings can be narrowed solely by emphasizing cognitive skills, said Christy Lleras, a University of Illinois assistant professor of human and community development.
“It’s important to note that good schools do more than teach reading, writing, and math. They socialize students and provide the kinds of learning opportunities that help them to become good citizens and to be successful in the labor market,” she said.
“Unless we address the differences in school climates and curriculum that foster good work habits and other social skills, we’re doing a huge disservice to low-income kids who may be entering the labor market right after high school, especially in our increasingly service-oriented economy,” Lleras added.
The University of Illinois study analyzed data from the National Educational Longitudinal Study, which followed a diverse group of 11,000 tenth graders for 10 years, tracking not only their scores on standard achievement tests but teacher appraisals of such qualities as the students’ work habits, their ability to relate well to peers, and their participation in extracurricular activities, a proxy for the ability to interact well with both students and adults.
The teachers’ assessments were then compared with the students’ self-reported educational attainments and earnings 10 years after high-school graduation. Even after controlling for students’ achievement test scores, family socioeconomic status, and educational attainment, Lleras found that such social skills as conscientiousness, cooperativeness, and motivation were as important as test scores for success in the workplace.
Related: Hands-on High School Engineering Education in Minnesota - building on students natural curiously - Fun k-12 Science and Engineering Learning
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“Edible Optics” Could Make Food Safer
Related: E. Coli Individuality - Science Fair Project on Bacterial Growth on Packaged Salads - Protecting the Food Supply - posts on food
The Nobel Prize in Chemistry 2008 is evenly shared by Osamu Shimomura, Boston University Medical School, USA; Martin Chalfie, Columbia University, New York, USA and Roger Y. Tsien, University of California, San Diego, USA for discovery and work with glowing green fluorescent protein.
The remarkable brightly glowing green fluorescent protein, GFP, was first observed in the beautiful jellyfish, Aequorea victoria in 1962. Since then, this protein has become one of the most important tools used in contemporary bioscience. With the aid of GFP, researchers have developed ways to watch processes that were previously invisible, such as the development of nerve cells in the brain or how cancer cells spread.
Tens of thousands of different proteins reside in a living organism, controlling important chemical processes in minute detail. If this protein machinery malfunctions, illness and disease often follow. That is why it has been imperative for bioscience to map the role of different proteins in the body.
This year’s Nobel Prize in Chemistry rewards the initial discovery of GFP and a series of important developments which have led to its use as a tagging tool in bioscience. By using DNA technology, researchers can now connect GFP to other interesting, but otherwise invisible, proteins. This glowing marker allows them to watch the movements, positions and interactions of the tagged proteins.
Researchers can also follow the fate of various cells with the help of GFP: nerve cell damage during Alzheimer’s disease or how insulin-producing beta cells are created in the pancreas of a growing embryo. In one spectacular experiment, researchers succeeded in tagging different nerve cells in the brain of a mouse with a kaleidoscope of colors.
Osamu Shimomura, a Japanese citizen, was born 1928 in Kyoto, Japan. He received his Ph.D. in organic chemistry 1960 from Nagoya University, Japan. first isolated GFP from the jellyfish Aequorea victoria, which drifts with the currents off the west coast of North America. He discovered that this protein glowed bright green under ultraviolet light.
Martin Chalfie demonstrated the value of GFP as a luminous genetic tag for various biological phenomena. In one of his first experiments, he coloured six individual cells in the transparent roundworm Caenorhabditis elegans with the aid of GFP.
Roger Y. Tsien contributed to our general understanding of how GFP fluoresces. He also extended the colour palette beyond green allowing researchers to give various proteins and cells different colours. This enables scientists to follow several different biological processes at the same time.
Related: 2007 Nobel Prize in Chemistry - Nobel Laureate Initiates Symposia for Student Scientists - Nobel Prize in Chemistry (2006) - Webcasts by Chemistry and Physics Nobel Laureates
Stanford gets $75 million for stem cell center
He said he was driven to fund research after President Bush, in August 2001, forbid the use of federal funds for stem cell research that involved the destruction of human embryos. “It’s very narrow-minded,” Lokey said of the position. “This is about lives being saved.”
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Some 350 scientists will work in the 200,000-square-foot Lorry I. Lokey Stem Cell Research Building, the school said. The center is also getting a $43.6 million grant from the California Institute for Regenerative Medicine. The institute, the state’s $3 billion stem cell funding unit, was created by a 2004 state initiative from research advocates opposed to Bush’s restrictions.
Related: Chinese Stem Cell Therapies - Scientists Cure Mice Of Sickle Cell Using Stem Cell Technique - Funding Medical Research - post on funding science
NSF Launches Third Generation of Engineering Research Centers with Awards Totaling $92.5 Million. Each of the 5 sites will receive will use $18.5 million over five-years. Each center has international university partners and partners in industry.
The NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), based at Iowa State University, seeks to transform the existing petrochemical-based chemical industry to one based on renewable materials.
The NSF Engineering Research Center for Future Renewable Electric Energy Delivery and Management (FREEDM) Systems, based at North Carolina State University, will conduct research to transform the nation’s power grid into an efficient network that integrates alternative energy generation and new storage methods with existing power sources.
The NSF ERC for Integrated Access Networks (CIAN), based at the University of Arizona, will conduct research to create transformative technologies for optical access networks that offer dramatically improved performance and expanded capabilities.
The NSF ERC for Revolutionizing Metallic Biomaterials, based at North Carolina Agricultural and Technical State University, aims to transform current medial and surgical treatments by creating “smart” implants for craniofacial, dental, orthopedic and cardiovascular interventions.
The NSF Smart Lighting ERC, based at Rensselaer Polytechnic Institute, aims to create new solid-state lighting technologies to enable rapid biological imaging, novel modes of communication, efficient displays and safer transportation.
Photo: Alex Huang will lead direct the research of ways to integrate renewable energy sources into the nation’s power grid at North Carolina State University.
Related: $75 Million for 5 New Engineering Research Centers - NSF Awards $50 Million for Collaborative Plant Biology Project - Presidential Early Career Award for Scientists and Engineers - posts related to the United States National Science Foundation
Ok, there really isn’t much new since I posted that holographic TV is getting closer. But won’t it be cool when I can have one in my house? And you might need to plan for it in your new house addition 
Also, with the economic news lately a good distraction might be useful - Holographic television to become reality
Dr Nasser Peyghambarian, chair of photonics and lasers at the university’s Optical Sciences department, told CNN that scientists have broken a barrier by making the first updatable three-dimensional displays with memory.
“This is a prerequisite for any type of moving holographic technology. The way it works presently is not suitable for 3-D images,” he said. The researchers produced displays that can be erased and rewritten in a matter of minutes.
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According to Peyghambarian, they could be constructed as a screen on the wall (like flat panel displays) that shows 3-D images, with all the image writing lasers behind the wall; or it could be like a horizontal panel on a table with holographic writing apparatus underneath.
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Peyghambarian is also optimistic that the technology could reach the market within five to ten years. He said progress towards a final product should be made much more quickly now that a rewriting method had been found.
However, it is fair to say not everyone is as positive about this prospect as Peyghambarian. Justin Lawrence, a lecturer in Electronic Engineering at Bangor University in Wales, told CNN that small steps are being made on technology like 3-D holograms, but, he can’t see it being ready for the market in the next ten years.
I would have to say I am with those that think this might take a bit longer to be in place. But I would be glad to be wrong.
Related: Video Goggles - Open Source for LEGO Mindstorms - posts on cool gadgets - Awesome Cat Cam
$400 million endowment for the Broad Institute of Harvard and MIT
Many countries would love to create a world class center of biomedical research. And several are trying. Boston sure seems to be staking a claim that it will be one of those centers of excellence. The economic benefits of that to Boston will be huge.
Related: Harvard Plans Life Sciences Campus - $1 Billion for Life Sciences in Massachusetts - China’s Gene Therapy Investment - $600 Million for Basic Biomedical Research from HHMI - Edinburgh University $115 Million Stem Cell Center
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