Botanists Develop 'Antifreeze' Spray for Plants

Posted on Thursday, September 16, 2010 by sai kiran reddy


Every year, Americans spend more than $38 billion on their lawns and gardens. No matter what you're growing, a sudden frost or freeze can spell serious trouble. Soon, science could come to the rescue with antifreeze for plants.
After 21 years in the nursery business, Margaret Brown knows cold can kill.
"We keep [our] fern houses on about 28 so they can take down a little below freezing," Brown said. Greenhouses keep Brown in business through the winter. For customers who spend hundreds -- even thousands -- on shrubs and flowers, the threat of a freeze is a serious issue.
"The phone rings constantly," Brown said. "I feel like a weatherman in the fall, because everybody wants to know what the weather's going to do."
"At minus 6.6 or minus 6.3 centigrade, plant tissues freeze solid, and we have to deal with that solidity, that freezing," said David Francko, Ph.D., a botanist at the University of Alabama in Tuscaloosa, Ala. Dr. Francko developed a solution that works like antifreeze for plants. It lowers the plants' freezing temperatures and enhances the plants' natural mechanisms to resist freeze damage.
"The ability to reduce the freezing point of water that's inside the tissues of that plant and also, once that water freezes, to allow that plant to survive freezing temperatures [helps]," Dr. Francko said. "It can be frozen solid and still be viable."
A freezing chamber put his freeze-proof solution to the test. Untreated, plant after plant couldn't make it below 30 degrees. Plants sprayed with the antifreeze solution survived the freeze with vital structures still intact. "It's like moving your whole home landscape about 200 miles farther south," Dr. Francko said. "That's about the effect that you get, anywhere from three to 10 degrees more cold tolerance."
As temperatures fall, a dose of antifreeze could buy gardeners and growers a little more time and a little more green. Dr. Green expects the product to be on the market for home and agricultural use by sometime this winter.
WHAT IS FREEZE PRUF? Freeze-Pruf combines five ingredients into a liquid spray to protect against cold damage in plants. The ingredients have a synergistic effect that exceeds the sum of what they would do individually. The ingredients include an antifreeze-like substance that is present in animals, another that helps to lower the freezing point of plant cells by dehydrating them, one that strengthens cell walls, another that helps the solution penetrate leaves, and one to resist washing away by rain and snow. The protection lasts about 4-6 weeks, and the best times to use it are the late fall and early spring.
WHAT IS FROST, AND HOW DOES IT FORM? Tiny frozen water droplets in the air make frost. When water changes to ice (or to steam, when heated) this is a process known as a "phase transition." When water reaches freezing temperature, it will turn into ice. Different materials freeze at different temperatures, but water at sea level will freeze at 32 degrees Fahrenheit. Humidity measures how much vapor is present in the air at any given time. Clear, calm fall nights, when the air mass is especially humid, are the best conditions for frost to form.
Frost is the frozen version of dew, and, like snow, it results from the presence of too much water vapor in already-saturated air. It is a very thin deposit of tiny ice crystals. Frost forms when water vapor in the air condenses directly into ice, instead of condensing first into a liquid, then into ice. Condensation typically occurs when the temperature drops sufficiently for the air to become saturated with water vapor. The excess vapor condenses onto surfaces colder than the air. If the surface temperature is above 32 degrees Fahrenheit, dew will form; if it is below 32 degrees Fahrenheit, frost will form.Frost forms on the inside surface of windowpanes when the air inside has lower humidity than the air outside. If it didn't, the water vapor would first condense into small drops before freezing into clear ice.

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Oral Biologists Use Chemistry To Formulate Cavity Fighting Mints

by sai kiran reddy


Sodas, candy and processed foods are packed with tooth-decaying, cavity-causing sugar. For the past 40 years, experts have seen a decrease in the amount of tooth decay in children; but according to Centers for Disease Control statistics, the trend is reversing. To tackle the problem, one dental scientist has found a way to use candy to help prevent cavities.
Tooth decay in kids has increased 28 percent in the past eight years. Experts believe too many sugary, processed foods and not enough brushing are to blame. A key factor in fighting cavities is found in your mouth.
"Saliva is the great protector against cavities," said Israel Kleinberg, D.D.S., Ph.D., an oral biologist at Stony Brook University in Stony Brook, N.Y.
Dr. Kleinberg says 40 years of research and more than $1 billion has been spent trying to figure out what saliva has that fights tooth decay.
"I'm one of the pioneers in that as a whole new science," Dr. Kleinberg said. "It's where one mixes dentistry and biochemistry."
Dr. Kleinberg discovered how saliva's chemistry helps teeth neutralize the acidity created from eating food by balancing the pH levels in the mouth.
"[It's] like if you've got a swimming pool," Dr. Kleinberg said. "You have got to get the pH right. If you've got a neutral pH, you've got the ideal condition."
He developed a candy to fight cavities. The candy is fluoride-free and protects teeth in two ways. First, it raises pH levels to neutralize more acid than saliva alone. Second, it protects the minerals in tooth enamel. Arginine, an amino acid, combines with calcium in Cavistat, the candy's main ingredient, and sticks to teeth -- leaving behind a layer of protection.
Kids who ate two mints twice a day for one year had 68 percent fewer cavities in their molars than children who didn't chew the mints.
"The number of cavities, we think that ultimately is going to get to almost zero," Dr. Kleinberg said.
That would bring a smile to just about everyone's face.
All the ingredients in the mints are natural and considered foods, so the product doesn't need FDA approval.
WHAT DOES IT DO? BasicMints contain Cavistat, a cavity-fighting agent that includes two major components. Cavistat disrupts oral chemistry and biology in two ways. First, it introduces an amino acid called arginine to the mouth. When bacteria in the mouth break the arginine down, it neutralizes the acid generated by sugars in food, which reduces the amount of acid in the mouth and helps prevent damage to teeth. Additionally the Cavistat adds other chemical compounds that protect the minerals that make up teeth from dissolving.
ANATOMY OF A TOOTH: We think of teeth as being the part visible above the gum, but this is only the tip, or crown, of a tooth. There is also a neck that lies at the gum line, and a root, located below the gum. The crown of each tooth has an enamel coating to protect the underlying dentine. Enamel is even harder than bone, thanks to rows of tightly packed calcium and phosphorus crystals. The underlying dentine is slightly softer, and contains tiny tubules that connect with the central nerve of the tooth within the pulp. The pulp forms the central chamber of the tooth, and is made of soft tissue containing blood vessels that carry nutrients to the tooth. It also contains nerves so teeth can sense hot and cold, as well as lymph vessels to carry white blood cells to fight bacteria.

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Plant Biologists And Immunochemists Develop Hypoallergenic Alternative To Latex

by sai kiran reddy


Since the 1980s, latex gloves have been an important part of preventing the spread of infectious diseases like MRSA, HIV and AIDS. In fact, ten billion latex gloves are used every year in the United States. As we use more latex, more people are developing dangerous allergies to it. Scientists have developed a new, natural alternative that may solve the problem.
Faith, Lamar and David Ryberg love games -- but that's not all they have in common. They all have Spina Bifida. Like 68 percent of kids with this birth defect, all three have dangerous allergies to latex.
"You just get kind of nervous you could stop breathing at any moment," Lamar said.
Three million Americans and as many as 17 percent of healthcare workers in the United States have latex allergies. Reactions range from skin irritations and wheezing to a sudden drop in blood pressure, anaphylactic shock and even death. Scientists say a desert plant called guayule offers a new, natural rubber alternative without the proteins that trigger allergic reactions.
Katrina Cornish, Ph.D., a plant biologist and immunochemist at the Yulex Corporation in Maricopa, Ariz., says the key to processing guayule is to release the rubber contained in the plant. It starts with a sort of guayule milkshake.
"We take the whole shrub and grind it up to release the rubber particles, which are made in the bark into an aqueous medium," said Dr. Cornish.
Rubber particles in the mixture are slightly lighter than water. By spinning the solution in a centrifuge, the rubber separates, forming a liquid that rises to the top. Dr. Cornish says not only is this latex alternative, called Yulex, safer for those with allergies -- products made with it are more flexible and stronger than latex. In this test, the Yulex on the left stood up to nearly twice as much force as the purple latex on the right.
Uses for guayule latex are virtually endless.
"So far, we haven't found anything made out of rubber that we can't make with guayule," Dr. Cornish said. It's a new kind of rubber that might just fit like a glove for the millions with latex allergies, like Lamar.
"It would be very, very good!" Lamar exclaimed.
Yulex recently received FDA approval for a medical examination glove. Researchers say it's comparable in price to high-end synthetic latex. Because over 50 percent of rubber products now available are petroleum-based, Yulex could become even more attractive as oil prices increase.
WHAT IS GUAYULE? Guayule is a plant native to North America that grows well in arid areas of the southwestern United States and in Mexico. The plant produces resins that act as natural pesticides, making guayule resistant to many pests and diseases. The bark of the guayule contains rubber, but it does not contain the allergy-causing proteins present in the plants that are used to make latex. Guayule rubber has comparable strength to that of synthetic latex, but is softer and more elastic.
WHAT ARE ALLERGIES? Every year, when spring rolls around, millions of Americans start sneezing and coughing. Allergies are the culprit. An allergy is simply a negative reaction to a substance that enters the body that is not toxic in itself, yet for some reason causes a bad reaction in the body. Just about anything can be an allergen: dust mites, pollen, cats, dogs, wasps or bees, milk, eggs, peanuts, and even fruits are the most common.
A normal immune system is the body's defense against invading bacteria and viruses. It senses potential invaders and attacks them by producing antibodies. But sometimes a person's immune system mistakes a common allergen as harmful. So it produces antibodies to attack them, and this triggers other cells to release chemicals called histamines, causing allergic symptoms. The most common symptoms of an allergic reaction include sneezing, swelling, itchy eyes, sinus pain, a runny nose, rashes or hives, coughing, and in some cases, vomiting. In extreme cases, an allergen can cause difficulty in breathing. This is called an anaphylactic reaction, and a severe attack can be fatal if not treated quickly.

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Biogeochemists Map Out Carbon Dioxide Emissions In The U.S.

by sai kiran reddy


The Environmental Protection Agency estimates emissions in the United States rose almost 15 percent between 1990 and 2006, and the number will continue to rise. Carbon dioxide is mainly responsible for the increase. A new high-tech map reveals the areas in the country most responsible for the carbon dioxide problem.
Carbon dioxide (CO2) is the most abundant greenhouse gas in our atmosphere. Its sources can be found almost everywhere -- from cars, to cows, to power plants -- but scientists are still trying to figure out which parts of the country are pumping out the most CO2.
In the past, CO2 levels have been calculated based on population, putting the Northeast at the top of the list. Now, a new map called Vulcan reveals for the first time where the top carbon dioxide producers are in the country. The answer surprised Kevin Gurney, Ph.D., a biogeochemist at Purdue University in West Lafayette, Ind.
"There are a lot more emissions in the Southeast than we previously thought, and a lot of that is because it's not necessarily associated with where people live directly, but actually where industry and activities are," said Dr. Gurney.
The high-resolution map shows 100 times more detail than ever before and zooms in to show greenhouse gas sources right down to factories, power plants and even roadways. An animated version of Vulcan reveals huge amounts of greenhouse gas gets blown toward the North Atlantic region.
"We've never had a map with this much detail and accuracy that everyone can view online," Dr. Gurney said.
The map helps scientists better visualize and target the areas where CO2 emissions are the highest and help those areas reduce their negative impact on Earth. It can be downloaded for free online from the Purdue University Vulcan Project Web site.
ABOUT CARBON DIOXIDE: The concentration of carbon dioxide in the atmosphere has increased by about 30 percent since the beginning of the industrial revolution in the late 1800's. Most of this increase comes from using fossil fuel -- coal, oil and natural gas -- for energy, but approximately 25 percent of the carbon came from changes in land use, such as the clearing of forests and the cultivation of soils for food production. Natural sources of atmospheric carbon include gases emitted by volcanoes, and respiration of living things. We breathe in oxygen, and breathe out carbon dioxide.
ABOUT AIR POLLUTION: Air pollution is made up of many kinds of gases, droplets and particles that can remain suspended in the air. This makes the air dirty. The easiest way to visualize airborne particles (also called aerosols) is to exhale outside on a cold day and watch the fog come out of your mouth as water vapor forms into water droplets. The same thing happens in the atmosphere, but for different reasons. Under certain conditions individual molecules come together and form particles -- a chemical soup. In the city, air pollution may be caused by cars, buses and airplanes, as well as industry and construction. Ground-level ozone is created when engine and fuel gases already released into the air interact when sunlight hits them. Ozone levels increase in cities when the air is stil

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CRISPR Critters: Scientists Identify Key Enzyme in Microbial Immune System

Posted on Wednesday, September 15, 2010 by sai kiran reddy


Through the combination of CRISPR and squads of CRISPR-associated -- "Cas" -- proteins, microbes are able to utilize small customized RNA molecules to silence critical portions of an invader's genetic message and acquire immunity from similar invasions in the future. To better understand how this microbial immune system works, scientists have needed to know more about how CRISPR's customized small RNA molecules get produced. Answers have now been provided by a team of researchers with the Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkeley.
In a study led by biochemist Jennifer Doudna, the research team used protein crystallography beamlines at Berkeley Lab's Advanced Light Source to produce an atomic-scale crystal structure model of an endoribonuclease called "Csy4." Doudna and her colleagues have identified Csy4 as the enzyme in prokaryotes that initiates the production of CRISPR-derived RNAs (crRNAs), the small RNA molecules that target and silence invading viruses and plasmids.
"Our model reveals that Csy4 and related endoribonucleases from the same CRISPR/Cas subfamily utilize an exquisite recognition mechanism to discriminate crRNAs from other cellular RNAs to ensure the selective production of crRNA for acquired immunity in bacteria," Doudna says. "We also found functional similarities between the RNA recognition mechanisms in Cys4 and Dicer, the enzyme that plays a critical role in eukaryotic RNA interference."
Doudna is a leading authority on RNA molecular structures who holds joint appointments with Berkeley Lab's Physical Biosciences Division and UC Berkeley's Department of Molecular and Cell Biology and Department of Chemistry. She is also an investigator with the Howard Hughes Medical Institute (HHMI). The results of this latest research on CRISPR are reported in the journal Science in a paper titled "Sequence- and structure-specific RNA processing by a CRISPR endonuclease." Co-authoring the paper with Doudna were Rachel Haurwitz, Martin Jinek, Blake Wiedenheft and Kaihong Zhou.
CRISPR is a unit of DNA, usually on a microbe's chromosome, made up of "repeat" elements, base-pair sequences ranging from 30 to 60 nucleotides in length, separated by "spacer" elements, variable sequences that are also from 30 to 60 nucleotides in length. CRISPR units are found in about 40-percent of all bacteria whose genomes have been sequenced, and about 90-percent of archaea. A microbe might have several CRISPR loci within its genome and each locus might contain between four and 100 CRISPR repeat-spacer units. Doudna and her colleagues studied CRISPR in Pseudomonas aeruginosa, a common bacterium that is ubiquitous in the environment.
Rachel Haurwitz, a graduate student in Doudna's research group and the first author on the Science paper, explains how the CRISPR/Cas immunity system works.
"When a bacterium recognizes that it has been invaded by a virus or a plasmid, it incorporates a small piece of the foreign DNA into one of its CRISPR units as a new spacer sequence. The CRISPR unit is then transcribed as a long RNA segment called the pre-crRNA. The Csy4 enzyme cleaves this pre-crRNA within each repeat element to create crRNAs about 60 nucleotides long that will contain sequences which match portions of the foreign DNA. Cas proteins will use these matching sequences to bind the crRNA to the invading virus or plasmid and silence it."
Haurwitz says the CRISPR/cas system for silencing foreign DNA in prokaryotes is analogous to the way in which short interfering or siRNAs correct genetic problems in eukaryotes. Over time, the CRISPR/cas system will build up inheritable DNA-encoded immunity from future invasions by the same types of viruses and plasmids.
With their crystal structure model of the Csy4 enzyme bound to its cognate RNA, which features a resolution of 1.8 Angstroms, the Berkeley CRISPR research team has shown that Csy4 makes sequence-specific interactions in the major groove of the CRISPR RNA repeat stem-loop. Together with electrostatic contacts to the phosphate backbone, these interactions enable Csy4 to selectively bind to and cleave pre-crRNAs using phylogenetically conserved residues of the amino acids serine and histidine in the active site.
"Our model explains sequence- and structure-specific processing by a large family of CRISPR-specific endoribonucleases," Doudna says.
Doudna and her colleagues produced their 1.8 Angstrom resolution crystallographic structure using the experimental end stations of Beamlines 8.2.1 and 8.3.1 at Berkeley Lab's Advanced Light Source (ALS). Both beamlines are powered by superconducting bending magnets -- "superbends" -- and both feature state-of-the-art multiple-wavelength anomalous diffraction (MAD) and macromolecular crystallography (MX) capabilities. Beamline 8.2.1 is part of the suite of protein crystallography beamlines that comprise the Berkeley Center for Structural Biology.
"The ALS and its protein crystallography beamlines continue to be a critical resource for our research, " Doudna says.
The crRNAs used by the CRISPR/cas system for the targeted interference of foreign DNA join the growing ranks of small RNA molecules that mediate a variety of processes in both eukaryotes and prokaryotes. Understanding how these small RNA molecules work can improve our basic understanding of cell biology and provide important clues to the fundamental role of RNA in the evolution of life.
Says Doudna, "By investigating how bacteria produce and use small RNAs for selective gene targeting, we hope to gain insight into the fundamental features of the pathways that have proven evolutionarily useful for genetic control, both in the bacterial world and in the world of eukaryotes. Right now it looks like bacteria and eukaryotes have evolved entirely distinct pathways by which RNAs are used for gene regulation and that is pretty amazing!"
This work was supported in part by grants from the National Science Foundation and from the Bill and Melinda Gates Foundation.

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Protein Clamps Tight to Telomeres to Help Prevent Aging and Support Cancer

by sai kiran reddy


While the nature of this portion of Cdc13 had previously eluded scientists, the Wistar researchers found that two copies of the protein bind together to form what is called a "dimer," and how that dimer physically interacts with DNA, regulating how enzymes called telomerases access and lengthen the telomeres. The study was performed using the yeast gene, however, this essential life process has changed little through evolution, and evidence suggests that the human equivalent of this protein may make a good target for future anticancer drugs.
They present their findings in the journal Molecular and Cellular Biology, available online now, ahead of print.
"Cdc13 has a crucial support role in maintaining and lengthening telomeres, which are reduced in length through every round of DNA replication," said Emmanuel Skordalakes, Ph.D., assistant professor in Wistar's Gene Expression and Regulation Program and senior author of the study. "We know that disabling this protein in humans will most likely lead to senescence, which is of particular interest in cancer, because telomere lengthening is one of the ways cancer cells obtain their immortality."
In the present study, Skordalakes and his colleagues detail how Cdc13 serves a dual function in telomere replication. First, it keeps the cells' natural DNA repair mechanisms from mistaking the telomere for a broken stretch of DNA, which could cause genetic mayhem if such repair proteins fuse the ends of two chromosomes together, for example. Secondly, Cdc13 recruits telomerase and related proteins to place in order to lengthen the telomeres.
When the researchers introduced mutations into Cdc13 that prevented the protein from forming a dimer, it caused the telomeres to shorten, which would hasten the demise of the yeast cells. When they created mutations that prevented Cdc13 dimers from binding to DNA, it had the effect of excessively lengthening telomeres, an act the researchers attribute to the notion that Cdc13 helps regulate the ability of DNA-replication enzymes to access telomeres. "The complex role of Cdc13 underscores the unique nature of telomeres and the fine balance between normal cell division and cancer," said Skordalakes.
Telomeres are important to cell division because they serve as sort of a timing mechanism that can, in effect, limit the number of times a normal cell can divide. As each cell divides, it must first replicate -- or copy -- the DNA of its chromosomes in exacting detail.
However, the proteins in cells that make this replication possible physically cannot copy the last few base units of DNA at the tips of the chromosomes, which effectively shortens the telomere each time a chromosome is copied. Without telomeres to serve as a buffer, a chromosome could conceivably lose a functioning gene as it is copied. This natural "lifespan" of cells was first identified in the 1960s as the Hayflick Limit, named after its discoverer, Leonard Hayflick, Ph.D., then a Wistar scientist.
In 2008, the Skordalakes laboratory was the first to determine the 3-D structure of the catalytic subunit of the enzyme telomerase, which functions to tack on the short stretches of DNA at the telomeres that the cell's main DNA-replicating enzymes miss. The act of preserving telomeres through telomerase is a hallmark of only certain cells, particularly those in developing embryos. In adults, telomerase is active in stem cells, certain immune system cells and, most notably, cancer cells.
According to Skordalakes, the discovery of the dimeric nature of Cdc13 sheds light into the core function of this protein, the recruitment of telomerase (which is also a dimer) to the telomeres. Within the Cdc13 dimer are multiple sites that can bind to DNA with varying degrees of affinity. This allows Cdc13 to straddle the DNA so that one section grips tightly to DNA, while another section -- with a more relaxed grip -- can bind nearer the tail end of the DNA strand and where telomerase binds. This feature of Cdc13 also assists in recruiting telomerase, summoning the enzyme into place above the telomere.
"You can think of Cdc13 as if it were you hanging on to the edge of a cliff, with one grip stronger than the other," Skordalakes said. "You're going to keep that strong hand on the cliff's edge while your weaker hand reaches into your pocket for your phone."
When Cdc13 interacts with telomerase, Skordalakes says, its weaker hand lets go of DNA, allowing the telomerase to access the telomere while the "strong hand" keeps the telomerase-Cdc13 complex firmly attached to the chromosome end. "It effectively serves as both a protective placeholder and a means of guiding telomerase activity," Skordalakes said.
The Skordalakes laboratory continues to explore the complex biology of telomeres, as well as the numerous other proteins necessary for telomere lengthening to occur. Meanwhile, they are investigating the potential of small molecule inhibitors to serve as viable therapeutics against cancer by blocking telomerase and their related proteins.
Co-authors from The Wistar Institute include David W. Speicher, Ph.D., a Wistar professor, and laboratory staff Meghan Mitchell (a former research assistant under Skordalakes), Mark Mason (a graduate student under Skordalakes), and Sandy Harper (a technician under Speicher ). They were joined by Jasmine S. Smith and F. Brad Johnson, M.D., Ph.D., from the University of Pennsylvania School of Medicine's Department of Pathology and Laboratory Medicine.
The research was supported by grants from the Pennsylvania Department of Health, The Ellison Medical Foundation, The Emerald Foundation, Inc., and the National Institute on Aging of the National Institutes of Health.

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Nature's Gift for Gardening May Hold Key to Biodiversity

by sai kiran reddy


DNA analysis of wild evergreen rhododendrons in the Himalayas has suggested that hundreds of species of the plant could be derived from hybrids -- cross-breeds between different species.
Their findings may help explain the rich biodiversity of the natural world, as it shows how random pairings of wild plants millions of years ago has led to the development of hundreds of new species that exist today.
While scientists have long known that single species can derive from hybrid origins, this latest finding offers rare evidence that whole groups of species can be developed from a hybrid ancestor.
Scientists sampled the DNA of 79 species of rhododendron and used the results to analyse how each species was related.
They found that although most Himalayan rhododendrons were descended from the same ancestral line, three rogue species showed traces of a second, distantly related ancestor. This species, now extinct, may have arrived in the Himalayas within the last 10 million years, and interbred with species already there.
The discovery suggests that much of the diversity found in rhododendrons -- and perhaps many other species -- is a result of ancient cross-breeding, which has enabled a diverse range of offspring over many successive generations.
The joint study with Royal Botanic Garden Edinburgh, published in the Journal of Plant Systematics and Evolution, was supported by the Natural Environment Research Council.
Dr Richard Milne of the University of Edinburgh's School of Biological Sciences, who led the research, said: "Nature seems to be more creative than the most gifted of gardeners. Cross-breeding in the wild may have played a significant part in contributing to the wealth of species on Earth today -- but more work is needed to investigate the significance of this.

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