Posts about basic research

Changing Life as We Know It

Update: Independent researchers find no evidence for arsenic life in Mono Lake

NASA has made a discovery that changes our understanding of the very makeup of life itself on earth. I think my favorite scientific discipline name is astrobiology. NASA pursues a great deal of this research not just out in space but also looking at earth based life. Their astrobiology research has changed the fundamental knowledge about what comprises all known life on Earth.

photo of Felisa Wolfe-Simon

Felisa Wolfe-Simon processing mud from Mono Lake to inoculate media to grow microbes on arsenic.

Carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur are the six basic building blocks of all known forms of life on Earth. Phosphorus is part of the chemical backbone of DNA and RNA, the structures that carry genetic instructions for life, and is considered an essential element for all living cells.

Phosphorus is a central component of the energy-carrying molecule in all cells (adenosine triphosphate) and also the phospholipids that form all cell membranes. Arsenic, which is chemically similar to phosphorus, is poisonous for most life on Earth. Arsenic disrupts metabolic pathways because chemically it behaves similarly to phosphate.

Researchers conducting tests in the harsh, but beautiful (see photo), environment of Mono Lake in California have discovered the first known microorganism on Earth able to thrive and reproduce using the toxic chemical arsenic. The microorganism substitutes arsenic for phosphorus in its cell components.

“The definition of life has just expanded,” said Ed Weiler, NASA’s associate administrator for the Science Mission Directorate. “As we pursue our efforts to seek signs of life in the solar system, we have to think more broadly, more diversely and consider life as we do not know it.” This finding of an alternative biochemistry makeup will alter biology textbooks and expand the scope of the search for life beyond Earth.

In science such huge breakthroughs are not just excepted without debate, however, which is wise.

Thriving on Arsenic:

In other words, every experiment Wolfe-Simon performed pointed to the same conclusion: GFAJ-1 can substitute arsenic for phosphorus in its DNA. “I really have no idea what another explanation would be,” Wolfe-Simon says.

But Steven Benner, a distinguished fellow at the Foundation for Applied Molecular Evolution in Gainesville, FL, remains skeptical. If you “replace all the phosphates by arsenates,” in the backbone of DNA, he says, “every bond in that chain is going to hydrolyze [react with water and fall apart] with a half-life on the order of minutes, say 10 minutes.” So “if there is an arsenate equivalent of DNA in that bug, it has to be seriously stabilized” by some as-yet-unknown mechanism.

It is sure a great story if it is true though. Other scientists will examine more data and confirm or disprove the claims.

“We know that some microbes can breathe arsenic, but what we’ve found is a microbe doing something new — building parts of itself out of arsenic,” said Felisa Wolfe-Simon, a NASA Astrobiology Research Fellow in residence at the U.S. Geological Survey in Menlo Park, Calif., and the research team’s lead scientist. “If something here on Earth can do something so unexpected, what else can life do that we haven’t seen yet?”
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All present-day Life on Earth Has A Single Ancestor

All present-day life arose from a single ancestor

All life on Earth shares a single common ancestor, a new statistical analysis confirms.

Because microorganisms of different species often swap genes, some scientists have proposed that multiple primordial life forms could have tossed their genetic material into life’s mix, creating a web, rather than a tree of life.

A universal common ancestor is at least 102,860 times more probable than having multiple ancestors, Theobald calculates.

For his analysis, Theobald selected 23 proteins that are found across the taxonomic spectrum but have structures that differ from one species to another. He looked at those proteins in 12 species – four each from the bacterial, archaeal and eukaryotic domains of life.

Then he performed computer simulations to evaluate how likely various evolutionary scenarios were to produce the observed array of proteins. Theobald found that scenarios featuring a universal common ancestor won hands down against even the best-performing multi-ancestor models.

Very interesting. Surprising too. As the article points out this doesn’t mean all life ever on Earth evolved from the single ancestor – life that has gone extinct could be from outside this single “tree.”

Related: Viruses and What is LifeEvolution is Fundamental to ScienceBacteria “Feed” on Earth’s Ocean-Bottom Crust

2009 Nobel Prize in Chemistry: the Structure and Function of the Ribosome

graphic image of the components of a cellCross section of a cell by the Royal Swedish Academy of Sciences. A ribosome is about 25 nanometters (a millionth of a millimeter) in size. A cell contains tens of thousands of ribosomes.

The Nobel Prize in Chemistry for 2009 awards studies of one of life’s core processes: the ribosome’s translation of DNA information into life. Ribosomes produce proteins, which in turn control the chemistry in all living organisms. As ribosomes are crucial to life, they are also a major target for new antibiotics.

This year’s Nobel Prize in Chemistry awards Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath for having showed what the ribosome looks like and how it functions at the atomic level. All three have used a method called X-ray crystallography to map the position for each and every one of the hundreds of thousands of atoms that make up the ribosome.

Inside every cell in all organisms, there are DNA molecules. They contain the blueprints for how a human being, a plant or a bacterium, looks and functions. But the DNA molecule is passive. If there was nothing else, there would be no life.

The blueprints become transformed into living matter through the work of ribosomes. Based upon the information in DNA, ribosomes make proteins: oxygen-transporting haemoglobin, antibodies of the immune system, hormones such as insulin, the collagen of the skin, or enzymes that break down sugar. There are tens of thousands of proteins in the body and they all have different forms and functions. They build and control life at the chemical level.

Related: The Nobel Prize in Chemistry 20082007 Nobel Prize in Chemistry2006 Nobel Prize in Chemistryposts on chemistrybasic research posts

Details from the Nobel Prize site (which continues to do a great job providing scientific information to the public openly).
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Image of the Common Cold Virus

image of the rhino virus (human cold)image created by Dr. Jean-Yves Sgro, Institute for Molecular Virology, University of Wisconsin-Madison, from published X-ray data. larger image

Sequences capture the code of the common cold

Conducted by teams at the University of Maryland School of Medicine, UW-Madison and the J. Craig Venter Institute, the work to sequence and analyze the cold virus genomes lays a foundation for understanding the virus, its evolution and three-dimensional structure and, most importantly, for exposing vulnerabilities that could lead to the first effective cold remedies.

“We’ve had bits and pieces of these things for a long time,” says Ann Palmenberg, of UW-Madison’s Institute for Molecular Virology and the lead author of the new study. “Now, we have the full genome sequences and we can put them into evolutionary perspective.”

As its name implies, the common cold is an inescapable, highly contagious pathogen. Humans are constantly exposed to cold viruses, and each year adults may endure two to four infections, while schoolchildren can catch as many as 10 colds.

“We know a lot about the common cold virus,” Palmenberg explains, “but we didn’t know how their genomes encoded all that information. Now we do, and all kinds of new things are falling out.”

The newly sequenced viruses also show, says Palmenberg, why it is unlikely we will ever have an effective, all-purpose cold vaccine: The existing reservoir of viruses worldwide is huge and, according to the new study, they have a tendency to swap genetic sequences when cells are infected by more than one virus, a phenomenon that can lead to new virus strains and clinical manifestations.

The ability of different cold virus strains to swap genes and make entirely new strains was thought to be impossible, notes Claire M. Fraser-Liggett, a co-author of the new study and director of the Institute for Genome Sciences and professor of medicine and microbiology at the University of Maryland School of Medicine. “There is the possibility that this could lead to the emergence of a new rhinovirus strain with fairly dramatic properties,” says Fraser-Liggett.

Related: Common Cold Alters the Activity of GenesLearning How Viruses Evade the Immune SystemLethal Secrets of 1918 Flu Virusimages of snowflakes

Image of Viral Coat

image of exterior of virus - made up of 5 million atomsHigh-energy X-ray diffraction was used to pinpoint some 5 million atoms in the protective protein coat of the PsV-F virus. The coat’s symmetrical features are shared by hundreds of viruses. The red and yellow sections illustrate how building blocks of four proteins come together to form the spherical shell.

The image reveals the structure of a type of protein coat shared by hundreds of known viruses containing double-stranded RNA genomes. The image was painstakingly created from hundreds of high-energy X-ray diffraction images and paints the clearest picture yet of the viruses’ genome-encasing shell called a “capsid.”

Viruses can reproduce themselves only by invading a host cell and highjacking its biochemical machinery. But when they invade, viruses need to seal off their genetic payload to prevent it from being destroyed by the cell’s protective mechanisms. Though there are more than 5,000 known viruses, including whole families that are marked by wide variations in genetic payload and other characteristics, most of them use either a helical or a spherical capsid.

“Spherical viruses like this have symmetry like a soccer ball or geodesic dome,” Pan said. “The whole capsid contains exactly 120 copies of a single protein.” Previous studies had shown that spherical capsids contain dozens of copies of the capsid protein, or CP, in an interlocking arrangement. The new research identified the sphere’s basic building block, a four-piece arrangement of CP molecules called a tetramer, which could also be building blocks for other viruses’ protein coats.

Full press release

Related: Viruses and What is LifeViruses Eating BacteriaMRI That Can See Bacteria, Virus and ProteinsFinding the Host Genes Viruses Require

Gene Duplication and Evolution

Roughly 10 million years ago, a major genetic change occurred in a common ancestor of gorillas, chimpanzees, and humans. Segments of DNA in its genome began to form duplicate copies at a greater rate than in the past, creating an instability that persists in the genome of modern humans and contributes to diseases like autism and schizophrenia. But that gene duplication also may be responsible for a genetic flexibility that has resulted in some uniquely human characteristics.

“Because of the architecture of the human genome, genetic material is constantly being added and deleted in certain regions,” says Howard Hughes Medical Institute investigator and University of Washington geneticist Evan Eichler, who led the project that uncovered the new findings. “These are really like volcanoes in the genome, blowing out pieces of DNA.”

Eichler and his colleagues focused on the genomes of four different species: macaques, orangutans, chimpanzees, and humans. All are descended from a single ancestral species that lived about 25 million years ago. The line leading to macaques broke off first, so that macaques are the most distantly related to humans in evolutionary terms. Orangutans, chimpanzees, and humans share a common ancestor that lived 12-16 million years ago. Chimps and humans are descended from a common ancestral species that lived about 6 million years ago.

By comparing the DNA sequences of the four species, Eichler and his colleagues identified gene duplications in the lineages leading to these species since they shared a common ancestor. They also were able to estimate when a duplication occurred from the number of species sharing that duplication. For example, a duplication observed in orangutan, chimpanzees, and humans but not in macaques must have occurred sometime after 25 million years ago but before the orangutan lineage branched off.

Eichler’s research team found an especially high rate of duplications in the ancestral species leading to chimps and humans, even though other mutational processes, such as changes in single DNA letters, were slowing down during this period.

Related posts: 8 Percent of the Human Genome is Old Virus GenesMutation Rate and EvolutionDNA Passed to Descendants Changed by Your Life
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Science Commons: Making Scientific Research Re-useful

Science Commons is a project of Creative Commons. Like other organizations trying to support the advancement of science with open access they deserve to be supported (PLoS and arXiv.org are other great organizations supporting science).

Science Commons has three interlocking initiatives designed to accelerate the research cycle – the continuous production and reuse of knowledge that is at the heart of the scientific method. Together, they form the building blocks of a new collaborative infrastructure to make scientific discovery easier by design.

Making scientific research re-useful, help people and organizations open and mark their research and data for reuse. Learn more.

Enabling one-click access to research materials, streamline the materials-transfer process so researchers can easily replicate, verify and extend research. Learn more.

Integrating fragmented information sources, help researchers find, analyze and use data from disparate sources by marking and integrating the information with a common, computer-readable language. Learn more.

NeuroCommons, is their proof-of-concept project within the field of neuroscience. The NeuroCommons is a beta open source knowledge management system for biomedical research that anyone can use, and anyone can build on.

Related: Open Source: The Scientific Model Applied to ProgrammingPublishers Continue to Fight Open Access to ScienceEncyclopedia of LifeScience 2.0 – Biology

How We Found the Missing Memristor

How We Found the Missing Memristor By R. Stanley Williams

For nearly 150 years, the known fundamental passive circuit elements were limited to the capacitor (discovered in 1745), the resistor (1827), and the inductor (1831). Then, in a brilliant but underappreciated 1971 paper, Leon Chua, a professor of electrical engineering at the University of California, Berkeley, predicted the existence of a fourth fundamental device, which he called a memristor. He proved that memristor behavior could not be duplicated by any circuit built using only the other three elements, which is why the memristor is truly fundamental.

the memristor’s potential goes far beyond instant-on computers to embrace one of the grandest technology challenges: mimicking the functions of a brain. Within a decade, memristors could let us emulate, instead of merely simulate, networks of neurons and synapses. Many research groups have been working toward a brain in silico: IBM’s Blue Brain project, Howard Hughes Medical Institute’s Janelia Farm, and Harvard’s Center for Brain Science are just three. However, even a mouse brain simulation in real time involves solving an astronomical number of coupled partial differential equations. A digital computer capable of coping with this staggering workload would need to be the size of a small city, and powering it would require several dedicated nuclear power plants.

Related: Demystifying the MemristorUnderstanding Computers and the Internet10 Science Facts You Should Know

Symptom of America’s Decline in Particle Physics

Land Of Big Science

Probing more deeply than ever before into the stuff of the universe requires some big hardware. It also requires the political will to lavish money on a project that has no predictable practical return, other than prestige and leadership in the branch of science that delivered just about every major technology of the past hundred years.

Those advances came, in large measure, from the United States. The coming decades may be different.

A third of the scientists working at the LHC hail from outside the 20 states that control CERN. America has contributed 1,000 or so researchers, the largest single contingent from any non-CERN nation.

The U.S. contribution amounts to $500 million—barely 5 percent of the bill. The big bucks have come from the Europeans. Germany is picking up 20 percent of the tab, the British are contributing 17 percent, and the French are giving 14 percent.

The most worrying prospect is that scientists from other countries, who used to flock to the United States to be where the action is, are now heading to Europe instead.

This is a point I have made before. The economic benefits of investing in science are real. The economic benefits of having science and engineering centers of excellence in your country are real. That doesn’t mean you automatically gain economic benefit but it is a huge advantage and opportunity if you act intelligently to make it pay off.

Related: Invest in Science for a Strong EconomyDiplomacy and Science ResearchAsia: Rising Stars of Science and EngineeringBrain Drain Benefits to the USA Less Than They Could Beposts on funding science explorationposts on basic researchAt the Heart of All Matter

Werner Heisenberg

photo of Werner Heisenberg

Read a very nice biography from Center for History of Physics of the American Institute of Physics for Werner Heisenberg, the founder of quantum mechanics, and the Heisenberg uncertainty principle:

Heisenberg set himself the task of finding the new quantum mechanics upon returning to Göttingen from Copenhagen in April 1925. Inspired by Bohr and his assistant, H.A. Kramers, in Copenhagen, Pauli in Hamburg, and Born in Göttingen, Heisenberg’s intensive struggle over the following months to achieve his goal has been well documented by historians. Since the electron orbits in atoms could not be observed, Heisenberg tried to develop a quantum mechanics without them.

He relied instead on what can be observed, namely the light emitted and absorbed by the atoms. By July 1925 Heisenberg had an answer, but the mathematics was so unfamiliar that he was not sure if it made any sense. Heisenberg handed a paper on the derivation to his mentor, Max Born, before leaving on a month-long lecture trip to Holland and England and a camping trip to Scandinavia with his youth-movement group. After puzzling over the derivation, Born finally recognized that the unfamiliar mathematics was related to the mathematics of arrays of numbers known as “matrices.” Born sent Heisenberg’s paper off for publication. It was the breakthrough to quantum mechanics.

Related: 1932 Nobel Prize in Physicsphoto, 1927Uncertainty: Einstein, Heisenberg, Bohr, and the Struggle for the Soul of Science by David Lindley – 2007 Nobel Prize in Physicsposts on physics

Microbes Beneath the Sea Floor

This stuff is cool. Here is the full press release from Penn State, Microbes beneath sea floor genetically distinct

Tiny microbes beneath the sea floor, distinct from life on the Earth’s surface, may account for one-tenth of the Earth’s living biomass, according to an interdisciplinary team of researchers, but many of these minute creatures are living on a geologic timescale.

“Our first study, back in 2006, made some estimates that the cells could double every 100 to 2,000 years,” says Jennifer F. Biddle, PhD. recipient in biochemistry and former postdoctoral fellow in geosciences, Penn State. Biddle is now a postdoctoral associate at the University of North Carolina, Chapel Hill.

The researchers looked at sediment samples from a variety of depths taken off the coast of Peru at Ocean Drilling Site 1229. They report their findings in today’s (July 22) online issue of the Proceedings of the National Academy of Sciences.

“The Peruvian Margin is one of the most active surface waters in the world and lots of organic matter is continuously being deposited there,” says Christopher H. House, associate professor of geoscience. “We are interested in how the microbial world differs in the subsea floor from that in the surface waters.”

The researchers used a metagenomic approach to determine the types of microbes residing in the sediment 3 feet, 53 feet, 105 feet and 164 feet beneath the ocean floor. The use of the metagenomics, where bulk samples of sediment are sequences without separation, allows recognition of unknown organism and determination of the composition of the ecosystem.

“The results show that this subsurface environment is the most unique environment yet studied metagenomic approach known today,” says House. “The world does look very different below the sediment surface.” He notes that a small number of buried genetic fragments exist from the water above, but that a large portion of the microbes found are distinct and adapted to their dark and quiet world.

The researchers, who included Biddle; House; Stephan C. Schuster, associate professor; and Jean E. Brenchley, professor, biochemistry and molecular biology, Penn State; and Sorel Fitz-Gibbon, assistant research molecular biologist at the Center for Astrobiology, UCLA, found that a large percentage of the microbes were Archaea, single-celled organisms that look like Bacteria but are different on the metabolic and genetic levels. The percentage of Archaea increases with depth so that at 164 feet below the sea floor, perhaps 90 percent of the microbes are Archaea. The total number of organisms decreases with depth, but there are lots of cells, perhaps as many as 1,600 million cells in each cubic inch.
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