Smart Economy

Oil and water: an icy interaction when oil chains are short, but steamy when chains are long

Purdue graduate student Joel Davis adjusts equipment used to identify a new structure water molecules assume when interacting with oil. (Purdue University photo/Mark Simons) Download Photo

WEST LAFAYETTE, Ind. — Water transforms into a previously unknown structure in between a liquid and a vapor when in contact with alcohol molecules containing long oily chains, according to Purdue University researchers. However, around short oily chains water is more icelike.

Water plays a huge role in biological processes, from protein folding to membrane formation, and it could be that this transformation is useful in a way not yet understood, said Dor Ben-Amotz, the professor of chemistry who led the research.

Ben-Amotz's research team found that as they examined alcohols with increasingly long carbon chains, the transformation occurred at lower and lower temperatures.

When in contact with a chain seven carbon atoms long, the water molecules became much looser and more vaporlike at a temperature of 140 degrees Fahrenheit, which is about halfway between the melting and boiling points.

"For oils with chains longer than four carbons, or about one nanometer in length, we saw the water transform into a completely new structure as the temperature rose," Ben-Amotz said. "If the trend we saw holds true, then this transformation could be happening at body temperature around important physiological molecules like proteins and phospholipids."

Dor Ben-Amotz (Purdue University photo/Steve Scherer) Download Photo

Water responds very sensitively in its structure to small changes, he said.

"Water's versatility is what makes it so special," he said. "For instance, the surfaces of proteins have both oily and charged regions; and water changes itself to accommodate these very different components and everything in between. We are learning more about exactly how it does this."

The researchers found that water molecules interacting with the oil always formed a more ordered, icelike structure at lower temperatures, while the bulk of the water remained liquid. This ice-like structure would melt away as the temperatures increased and in longer molecules a new structure would appear, he said.

A paper detailing the National Science Foundation-funded work is published in the current issue of Nature and is also highlighted in a news and views article in the same issue. In addition to Ben-Amotz, co-authors include Purdue graduate student Joel Davis and postdoctoral fellows Kamil Gierszal and Ping Wang.

The team's observations add to a more than 70-year debate over the interaction of oil and water, with some studies suggesting that water forms little icebergs around the oil molecules, while others point to a more disordered, vaporlike water structure.

"This question was really up for grabs until we introduced an experimental method that could see these subtle changes in water structure," Ben-Amotz said. "Surprisingly, we found that both sides are right, and it depends on the size of the oil."

The challenge of the experiment was that the team needed to see the very small number of water molecules that are in contact with the oil chains in the presence of a very large number of other water molecules.

The team combined Raman scattering and multivariate curve resolution to create an analysis method capable of managing an unprecedented signal-to-noise ratio of 10,000-to-1.

"Most people never take a spectrum with a signal-to-noise ratio greater than 100-to-1, but if we performed this experiment that way we wouldn't see anything," Ben-Amotz said. "We needed to have a higher signal-to-noise ratio because we were looking for a needle in a mountain-sized haystack."

Raman scattering involves shooting a beam of light containing photons into a sample. As the photons hit molecules within the sample, they lose or gain energy. Such measurements create a spectrum of peaks that reveal the vibrational motions of the molecules present in the sample. Shifts in the peaks' shapes can show changes in the strength of bonds between water molecules and whether the molecules are becoming more or less ordered.

"With Raman scattering the bulk of the water creates a mountainous peak in the spectrum that buries everything else," Ben-Amotz said. "Multivariate curve resolution lets us see small changes in water structure under that mountain. As is often the case in science, the key was combining two already established techniques in a new way."

Davis said the team next plans to explore the effects of changes in pH and ionic charges on this transformation with the goal of making the experiments more relevant to proteins and biological systems.

"We are trying to better understand the driving forces of the behavior of proteins and cell membranes that are critical to our health," he said. "The role of water is an important piece of the puzzle."

Writer: Elizabeth K. Gardner, 765-494-2081,[email protected]

Sources: Dor Ben-Amotz, 765-494-5256, [email protected]

Joel Davis, [email protected]

Related website:
Be-Amotz research group

---

ABSTRACT

Water structural transformation at molecular hydrophobic interfaces

Joel G. Davis, Kamil P. Gierzal, Ping Wang & Dor Ben-Amotz

Hydrophobic hydration is considered to have a key role in biological processes ranging from membrane formation to protein folding and ligand bonding. Historically, hydrophobic hydration shells were thought to resemble solid clathrate hydrates, with solutes surrounded by polyhedral cages composed of tetrahedrally hydrogen bonded water molecules. But more recent experimental and theoretical studies have challenged this view and emphasized the importance of the length scales involved. Here, we report combined polarized, isotopic and temperature-dependent Raman scattering measurements with multivariate curve resolution (Raman-MCR) that explore hydrophobic hydration by mapping the vibrational spectroscopic features arising from the hydrophobic hydration shells of linear alcohols ranging from methanol to heptanol. Our data, covering the entire 0-100 degrees Celsius temperature range, show clear evidence that at low temperatures the hydration shells have a hydrophobically enhanced water structure with greater tetrahedral order and fewer weak hydrogen bonds than the surrounding bulk water. This structure disappears with increasing temperature and is then, for hydrophobic chains longer than ~1nm, replaced by a more disordered structure with weaker hydrogen bonds than bulk water. These observations support our current understanding of hydrophobic hydration, including the thermally induced water structural transformation that is suggestive of the hydrophobic crossover predicted to occur at lengths of ~1nm.

DNA imaged with electron microscope for the first time

December 2, 2012

(Credit: Francesco Gentile et al./Nano Letters)

An electron microscope has imaged threads of DNA directly or the first time, New Scientist reports.

The technique will let researchers see how proteins, RNA and other biomolecules interact with DNA.

The structure of DNA was originally discovered using X-ray crystallography, requiring complex mathematics to reconstruct the crystal structure from the observed patterns.

The new images are a direct picture of the DNA strands, seen with electrons rather than X-ray photons. The trick used by Enzo di Fabrizio at the University of Genoa, Italy, and his team was to snag DNA threads out of a dilute solution and lay them on a bed of nanoscopic silicon pillars. The results reveal the corkscrew thread of the DNA double helix, clearly visible.

Using more sensitive detectors that can respond to lower-energy electrons should soon allow the team to see individual double helices, and even unwound single strands of DNA. 

REFERENCES:

• Francesco Gentile et al., Direct Imaging of DNA Fibers: The Visage of Double Helix, Nano Letters, 2012, DOI: 10.1021/nl3039162

Smart Bio Plastics from CO2 Flue Gas

Oakbio Makes Bioplastic at Cement Plant using

CO2 from Flue Gas and Electricity 

Milestone for cement industry
and renewable products

 

SUNNYVALE, CA (July 10,  2012) - Today Oakbio Inc.

announced the successful production of bioplastic

polymers in their bioreactor systems. Oakbio's

system creates bioplastic using inputs of cement

plant flue gas and electricity. The technology
uses bioreactors driven by non-toxic microbes

to capture CO2 and convert it to a variety of

sustainable products directly from the plant's

gas emissions.

 

This is the latest  development from an on-site

research collaboration at Lehigh Southwest Cement
Company's Permanente cement manufacturing

plant in Cupertino. Lehigh Southwest is part of

Lehigh Hanson, Inc., the North American operations

of the  Heidelberg Cement Group, a world leader

in construction materials with  approximately

52,000 employees in more than 40 countries.

 

Chief Scientist Brian
Sefton stated, "Our carbon conversion process

yields over 50% bioplastics in  microbe biomass

by dry weight from inputs of raw flue gas and

electricity. The type of plastic we make is not

only renewable, but biodegradable as
well.

 

"The effective conversion of captured CO2 into

a valuable bioplastic product represents an

important technical achievement for potential

large-scale bioplastics production. This result

also points the way to a new method for

greenhouse gas capture, making emissions

gas CO2 a feedstock for mass scale manufacturing."

 

CEO Russell Howard added:
"At Oakbio we see industrial CO2 as a carbon

resource. By converting virtually unlimited amounts

of low cost CO2 available from various industries

worldwide into sustainable products like biodegradable

plastics, Oakbio's technology can answer multiple

needs: full scale chemicals production without the

use of petroleum oil or agricultural feedstock;

replacement of petroleum oil-derived plastics

with bio-degradable renewable products; and

the capture of CO2 to prevent greenhouse gas

accumulation. The ability of our microbes to

perform their magic in cement flue gas is an

important step toward achieving this vision".

 

 

About Oakbio, Inc.

Oakbio is a private
technology-based company in Sunnyvale dedicated to sustainable production of
specialty chemicals using novel microbial production processes that combine GHG
reduction with manufacture of sustainable specialty chemicals (see www.oakbio.com).

Media
Contact:

Russell Howard, CEO,
Oakbio, (408) 930-7004; [email protected]

Smart Bio Plastics from CO2 Flue Gas

Oakbio Makes Bioplastic at
Cement Plant using CO2 from Flue Gas and Electricity 

Milestone for cement industry
and renewable products

 

SUNNYVALE, CA (July 10,  2012) - Today Oakbio Inc. announced the successful production of
bioplastic polymers in their bioreactor systems. Oakbio's system creates
bioplastic using inputs of cement plant flue gas and electricity. The technology
uses bioreactors driven by non-toxic microbes to capture CO2 and convert it to a
variety of sustainable products directly from the plant's gas
emissions.

 

This is the latest
development from an on-site research collaboration at Lehigh Southwest Cement
Company's Permanente cement manufacturing plant in Cupertino. Lehigh Southwest
is part of Lehigh Hanson, Inc., the North American operations of the
HeidelbergCement Group, a world leader in construction materials with
approximately 52,000 employees in more than 40 countries.

 

Chief Scientist Brian
Sefton stated, "Our carbon conversion process yields over 50% bioplastics in
microbe biomass by dry weight from inputs of raw flue gas and electricity. The
type of plastic we make is not only renewable, but biodegradable as
well.

 

"The effective conversion
of captured CO2 into a valuable bioplastic product represents an important
technical achievement for potential large-scale bioplastics production. This
result also points the way to a new method for greenhouse gas capture, making
emissions gas CO2 a feedstock for mass scale manufacturing."

 

CEO Russell Howard added:
"At Oakbio we see industrial CO2 as a carbon resource. By converting virtually
unlimited amounts of low cost CO2 available from various industries worldwide
into sustainable products like biodegradable plastics, Oakbio's technology can
answer multiple needs: full scale chemicals production without the use of
petroleum oil or agricultural feedstock; replacement of petroleum oil-derived
plastics with bio-degradable renewable products; and the capture of CO2 to
prevent greenhouse gas accumulation. The ability of our microbes to perform
their magic in cement flue gas is an important step toward achieving this
vision".

 

 

About Oakbio, Inc.

Oakbio is a private
technology-based company in Sunnyvale dedicated to sustainable production of
specialty chemicals using novel microbial production processes that combine GHG
reduction with manufacture of sustainable specialty chemicals (see www.oakbio.com).

Media
Contact:

Russell Howard, CEO,
Oakbio, (408) 930-7004; [email protected]

How antiseptic proteins in teardrops, lysozymes annihilate harmful bacteria

UCI team discovers how protein in teardrops annihilates harmful bacteria

Finding that lysozymes have jaws could aid in early diagnosis of cancer

Irvine, Calif. – A disease-fighting protein in our teardrops has been tethered to a tiny transistor, enabling UC Irvine scientists to discover exactly how it destroys dangerous bacteria. The research could prove critical to long-term work aimed at diagnosing cancers and other illnesses in their very early stages.

Ever since Nobel laureate Alexander Fleming found that human tears contain antiseptic proteins called lysozymes about a century ago, scientists have tried to solve the mystery of how they could relentlessly wipe out far larger bacteria. It turns out that lysozymes have jaws that latch on and chomp through rows of cell walls like someone hungrily devouring an ear of corn, according to findings that will be published Jan. 20 in the journal Science.

"Those jaws chew apart the walls of the bacteria that are trying to get into your eyes and infect them," said molecular biologist and chemistry professor Gregory Weiss, who co-led the project with associate professor of physics & astronomy Philip Collins.

The researchers decoded the protein's behavior by building one of the world's smallest transistors – 25 times smaller than similar circuitry in laptop computers or smartphones. Individual lysozymes were glued to the live wire, and its eating activities were monitored.

"Our circuits are molecule-sized microphones," Collins said. "It's just like a stethoscope listening to your heart, except we're listening to a single molecule of protein."

It took years for the UCI scientists to assemble the transistor and attach single-molecule teardrop proteins. The scientists hope the same novel technology can be used to detect cancerous molecules. It could take a decade to figure out, but would be well worth it, said Weiss, who lost his father to lung cancer.

"If we can detect single molecules associated with cancer, then that means we'd be able to detect it very, very early," Weiss said. "That would be very exciting, because we know that if we treat cancer early, it will be much more successful, patients will be cured much faster, and costs will be much less."

 

###

 

The project was sponsored by the National Cancer Institute and the National Science Foundation. Co-authors of the Science paper are Yongki Choi, Issa Moody, Patrick Sims, Steven Hunt, Brad Corso and Israel Perez.

About the University of California, Irvine: Founded in 1965, UCI is a top-ranked university dedicated to research, scholarship and community service. Led by Chancellor Michael Drake since 2005, UCI is among the most dynamic campuses in the University of California system, with nearly 28,000 undergraduate and graduate students, 1,100 faculty and 9,000 staff. Orange County's second-largest employer, UCI contributes an annual economic impact of $4 billion. For more UCI news, visit www.today.uci.edu.

News Radio: UCI maintains on campus an ISDN line for conducting interviews with its faculty and experts. Use of this line is available for a fee to radio news programs/stations that wish to interview UCI faculty and experts. Use of the ISDN line is subject to availability and approval by the university.

UCI maintains an online directory of faculty available as experts to the media. To access, visit www.today.uci.edu/experts. For UCI breaking news, visit www.zotwire.uci.edu.

'Green' chemical production via natural biochemical refineries

Same fungus, different strains

A comparative genomics approach for improved 'green' chemical production

Fungi play key roles in nature and are valued for their great importance in industry. Consider citric acid, a key additive in several foods and pharmaceuticals produced on a large-scale basis for decades with the help of the filamentous fungus Aspergillus niger. While A. niger is an integral player in the carbon cycle, it possesses an arsenal of enzymes that can be deployed in breaking down plant cell walls to free up sugars that can then be fermented and distilled into biofuel, a process being optimized by U.S. Department of Energy researchers.

Published online ahead of print May 4, 2011 in Genome Research, a team led by Scott Baker of the Pacific Northwest National Laboratory compared the genome sequences of two Aspergillus niger strains to, among other things, better harness its industrial potential in biofuels applications. As more than a million tons of citric acid are produced annually, the production process involving A. niger is a well understood fungal fermentation process that could inform the development of a biorefinery where organic compounds replace the chemical building blocks normally derived from petroleum. Learning more about the genetic bases of the behaviors and abilities of these two industrially relevant fungal strains, wrote senior author Baker and his colleagues in the paper, will allow researchers to exploit their genomes towards the more efficient production of organic acids and other compounds, including biofuels.

"Aspergillus niger is an industrial workhouse for enzymes and small molecules such as organic acids," said Baker of the fungus selected for sequencing by the DOE JGI in 2005. "Most of the world's citric acid comes from A. niger. "We know that this single organism is used for production of organic acids and for enzymes, and it can degrade plant cell wall matter for sugar production," said Baker. "For biofuels it's a highly relevant organism since it's already been scaled up, shown to be safe, and used for enzyme production. That's why it was such an important organism to further characterize through DNA sequencing."

The DOE Joint Genome Institute (JGI) generated the 35-million base genome of A. niger ATCC 1015, the wild type strain that was used in research that led to the first patented citric acid process. The other A. niger strain used in the study was sequenced by a company in the Netherlands in 2007 and has undergone mutagenesis and selection for enzyme production.

By analyzing the genomes on several levels—DNA, chromosome, gene and protein—Baker and his colleagues found several hundred unique genes in each strain that are key to their predominant characteristics. For example, A. niger ATCC 1015 had a higher expression of traits involved in high citric acid yields. On the other hand, the induced mutant strain had more elements related to efficient enzyme production. The team also noted that the genes involved in boosting enzyme production in the induced mutant strain of A. niger may have come from another Aspergillus strain via horizontal gene transfer, which allows one organism to acquire and use genes from other organisms.

Of the 47 authors on this paper, 30 are from Europe. "This is an excellent example of international collaboration combining genome sequencing with functional genomics, transcriptomics and metabolomics, which led to a system level study and comparative analysis of two A. niger strains," said study co-author Igor Grigoriev, head of the DOE JGI Fungal Genomics Program. "Nearly a dozen additional Aspergillus strains that are used in industry are either being sequenced or in the queue to be at the DOE JGI. A better understanding of genomic content and organization and how rearrangements and mutations lead to desired traits should facilitate further optimization of these strains for different bio-products."

As of 2007, the global market for citric acid was estimated to be approximately $1.2 billion with more than 500,000 tons produced annually by fermentation. "Having the genetic blueprint for a citric acid-producing fungus will increase our understanding of the organism's metabolic pathways that can be fine-tuned to enhance productivity or alter its metabolism to generate other green chemicals and fuels from renewable and sustainable plant-derived sugars," said Randy Berka, Director, Novozymes, Inc., and one of the publication's authors.

"It was thought that if we understood what makes the citric acid process so productive, then we could start to understand how to make other organic acids that could be commodity chemicals," said Baker. "We now have the tools and the foundation of knowledge to be able to ask some additional important questions that we weren't equipped with the genomic resources to answer before."

 Walter Derzko

Smart Economy

Toronto

The role of metabolism in disease

Thematic program focuses on cells' energy currency, communications and cancer

WASHINGTON, April 7, 2011 – Metabolism encompasses the biochemical reactions that sustain life and is usually thought of as two complementary systems: one that breaks down nutrients to generate energy and another that harnesses this energy to produce the building blocks cells need to thrive. Considering the fundamental importance of this chemical give-and-take, it's not surprising that metabolic dysfunctions can lead to serious diseases.

Next week, experts on metabolism will convene for a thematic program, at the American Society for Biochemistry and Molecular Biology's annual meeting at the Experimental Biology 2011 conference in Washington, D.C., to discuss scientific advances in understanding the links between metabolic function and the onset of disease. Theme organizers Barbara E. Corkey from the Boston University School of Medicine and Marc Prentki from the University of Montreal have invited an international team of scientists to present their recent findings on this medically important topic in Room 202B of the Walter E. Washington Convention Center.

 

 

 

 

Mitochondrial Function and Disease:

The first platform session will be held from 3:45 p.m. to 6 p.m. Sunday and will focus on mitochondria, the "powerhouses" of cells, which generate ATP, the cell's basic unit of energy currency. In this session, two researchers, one from the University of Miami and another from McGill University, will present their research linking mitochondrial dysfunction to aging. A third presenter from Boston University will discuss studies with mice that have mitochondrial mutations that lead to obesity and hyperglycemia.

Workshop — Measuring Mitochondrial Function and Dysfunction:

In addition to the regular platform sessions, this thematic program also will feature a workshop from 6:30 p.m. to 7:30 p.m. Sunday. Participants can review the principles of measuring mitochondrial function and dysfunction and learn about the newest tools available in the field.

Metabolic Communication:

The second round of talks, to be held from 9:55 a.m. to 12:10 p.m. Monday, will examine the role of communication between cells in age-related diseases as well as obesity and insulin resistance. The three talks will feature researchers from Emory University, the University of Alabama at Birmingham and the University of Southern California Medical School.

Metabolic Signal Transduction:

The third platform session in the program will be held from 3:45 p.m. to 6 p.m. Tuesday and will focus on how cells communicate their energy needs. Insulin acts like a fuel gauge for cells, signaling when the cell has too much or not enough energy, and works in concert with other chemical signals to maintain healthy cellular function. This session will feature research on three different metabolic signaling systems and their roles in obesity, diabetes and metabolic disease. Scientists from the University of Montreal, Boston University School of Medicine and the École Polytechnique Fédérale de Lausanne in Switzerland will speak.

Metabolism and Cancer:

The final round of talks, to be held from 9:55 a.m. to 12:10 p.m. Wednesday, will feature recent discoveries concerning metabolism and cancer. Metabolic processes are critical to the survival and growth of cancer cells, and exciting new research is investigating the metabolic functions that can contribute to cancer development and potential mechanisms for prevention. This session will include presentations by researchers from the University of Pennsylvania, University of Toronto and McGill University.

 

###

 

About Experimental Biology 2011

Experimental Biology is an annual gathering of six scientific societies that this year is expected to draw 13,000-plus independent scientists and exhibitors. The American Society for Biochemistry and Molecular Biology (ASBMB) is a co-sponsor of the meeting, along with the American Association of Anatomists (AAA), American Physiological Society (APS), American Society for Investigative Pathology (ASIP), American Society for Nutrition (ASN) and the American Society for Pharmacology and Experimental Therapeutics (ASPET).

More information about EB2011 for the media can be found on the press page: http://experimentalbiology.org/content/PressInformation.aspx.

About the American Society for Biochemistry and Molecular Biology

The ASBMB is a nonprofit scientific and educational organization with more than 12,000 members worldwide. Most members teach and conduct research at colleges and universities. Others conduct research in various government laboratories, at nonprofit research institutions and in industry. The Society's student members attend undergraduate or graduate institutions. For more information about ASBMB, visit www.asbmb.org.

Scientists create world's first 'super-twisted' light

The research team at the University of Glasgow twisted the light like a corkscrew by using a polarising filter, before shining it onto a specially shaped piece of gold to create the world's first 'super twisting'.

Super twisted light does not exist in nature and, until now, it had only been theorised by scientists, never produced.

Super twisted light can be used to find protein traces in incredibly small samples of biological material  like blood, far less than currently used.

The researchers have already used the light to look at many different proteins and have found that it is particularly sensitive to the structures of proteins which cause degenerative diseases such as Alzheimer’s and Parkinson’s Disease.

The findings have been published in Nature Nanotechnology.

Dr Malcolm Kadodwala, senior lecturer in the School of Chemistry, said: “We are very excited by this research. Essentially, this twisted light, which does not exist naturally, allows us to detect biological materials at unprecedented low concentrations.

“Due to the nature of the twisted light, it has been shown to be particularly effective at detecting proteins with a structure characteristic of amyloids – insoluble proteins that can stick together to form plaques within different organs in the body.

“It is these plaques which are thought to play a part in neurodegenerative diseases such as Alzheimer’s, Parkinson’s and CJD – though the reasons for this are unclear.

“We’re now looking to see if this same technique can be adapted to detect a wider range of proteins which are indicative of other diseases. The fact this method requires much less material (just one picogram or million millionth of a gram) for analysis than current techniques and uses a form of light previously unrealised is a big step forward.”

The complex science behind the technique takes advantage of the fact light can be twisted like a corkscrew by passing it through a special polarising filter: in much the same way as polarised sunglasses allow only certain alignments of light waves through.

By shining light onto a specially-shaped piece of metal – in this case gold – the light that is emitted from the metal becomes super-twisted.

Polarised or twisted light is already used in some medical techniques to analyse biomolecules, however the multidisciplinary Glasgow team, have been able to achieve a much more powerful system by twisting the light even tighter.

The team included engineer Dr Nikolaj Gadegaard and life scientist, Dr Sharon Kelly, with a team of physicists at the University of Exeter, led by Dr Euan Hendry.

The use of super-twisted light in spectroscopy – the analysis of materials according to way they absorb and emit light – has numerous potential applications in biosensing and could also be used to detect particular types of viruses which have similar structures.

Provided by University of Glasgow

Semi-synthetic Life; Scientists swap entire natural bacterial genome for artificial man-made genome

Scientist Craig Ventner and his team have inserted an entire synthetic genome into  bacterial cells, that took over the operation of the cell from the natural genome. This follows previous successes in inserting snipets in DNA from species to species and transplanting the entire natural genome from one bacterial species into another.

Significance:

This could be rated as one of top 5 discoveries for 2010.

Proof of concept  that bacterila genomes can be swapped by synthetic versions of entire genomes. Leads to the next stage-interting unique bio-apps in to bacterial, viruses, fungi or algae-.like new apps (applications) for your smart i-phone. Creating semi artificail bacterial or algae that convert C02 in butyl alcohols or higher chain gasoline or gasohol. (ETA 2015-2020)

Will we be seeing basement biologists hacking and tinkering with life? Not very soon. A Science Commentary this week reports:

"The synthetic genome created by Venter's team is almost identical to that of a natural bacterium. It was achieved at great expense, an estimated $40 million, and effort, 20 people working for more than a decade. Despite this success, creating heavily customized genomes, such as ones that make fuels or pharmaceuticals, and getting them to "boot" up the same way in a cell is not yet a reality. "There are great challenges ahead before genetic engineers can mix, match, and fully design an organism's genome from scratch," notes Paul Keim, a molecular geneticist at Northern Arizona University in Flagstaff."

Background:

Negatively stained transmission electron micrographs of dividing M. mycoides JCVI-syn1. Electron micrographs were provided by Tom Deerinck and Mark Ellisman of the National Center for Microscopy and Imaging Research at the University of California at San Diego.

(PhysOrg.com) -- Scientists have developed the first cell controlled by a synthetic genome. They now hope to use this method to probe the basic machinery of life and to engineer bacteria specially designed to solve environmental or energy problems.

The study will be published online by the journal Science, at the Science Express website, on Thursday, 20 May.

The research team, led by Craig Venter of the J. Craig Venter Institute, has already chemically synthesized a bacterial genome and it has transplanted the genome of one bacterium to another. Now, the scientists have put both methods together, to create what they call a "synthetic cell," although only its genome is synthetic.

"This is the first synthetic cell that's been made, and we call it synthetic because the cell is totally derived from a synthetic chromosome, made with four bottles of chemicals on a chemical synthesizer, starting with information in a computer," said Venter.

"This becomes a very powerful tool for trying to design what we want biology to do. We have a wide range of applications [in mind]," he said.

For example, the researchers are planning to design algae that can capture carbon dioxide and make new hydrocarbons that could go into refineries. They are also working on ways to speed up vaccine production. Making new chemicals or food ingredients and cleaning up water are other possible benefits, according to Venter.

In the Science study, the researchers synthesized the genome of the bacterium M. mycoides and added DNA sequences that "watermark" the genome to distinguish it from a natural one.

Because current machines can only assemble relatively short strings of DNA letters at a time, the researchers inserted the shorter sequences into yeast, whose DNA-repair enzymes linked the strings together. They then transferred the medium-sized strings into E. coli and back into yeast. After three rounds of assembly, the researchers had produced a genome over a million base pairs long.
 

The scientists then transplanted the synthetic M. mycoides genome into another type of bacteria, Mycoplasm capricolum. The new genome "booted up" the recipient cells. Although fourteen genes were deleted or disrupted in the transplant bacteria, they still looked like normal M. mycoides bacteria and produced only M. mycoides proteins, the authors report.

Enlarge

The assembly of a synthetic M. mycoides genome in yeast. Figure from Gibson, D. G., J. I. Glass, et al. 2010. Creation of a bacterial cell controlled by a chemically synthesized genome. Science, Published online May 20 2010.

"This is an important step we think, both scientifically and philosophically. It's certainly changed my views of the definitions of life and how life works," Venter said.

Acknowledging the ethical discussion about synthetic biology research, Venter explained that his team asked for a bioethical review in the late 1990s and has participated in variety of discussions on the topic.

"I think this is the first incidence in science where the extensive bioethical review took place before the experiments were done. It's part of an ongoing process that we've been driving, trying to make sure that the science proceeds in an ethical fashion, that we're being thoughtful about what we do and looking forward to the implications to the future," he said.

More information: 20 May 2010, Science, "Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome."
J. Craig Venter Institute announcement: http://www.jcvi.org/cms/press/press-releases/full-text/article/first-self-replicating-synthetic-bacterial-cell-constructed-by-j-craig-venter-institute-researcher/

Provided by American Association for the Advancement of Science

Hydrated Fullerenes (C60-HyFn) attack blood clots or deep vein thrombosis (DVT)

UPDATE  Nov 2010: HYFNs have been approved for manufacturing as Fullerene Water Solution (FWS)  drink in Ukraine by the  Ministry of Health  as of Nov 2010. It's the first nanotech based health drink in the world. For information about availability  contact me privately by email.

In June 2008, Ukrainian researchers published a little noticed and rarely cited article in a Ukrainian medical journal called Medical Chemistry  ( Медична Хімія) on research done back in 2007 and earlier.

The intriguing title?  "THE ACCELERATION OF BLOOD PLASMA CLOT LYSIS IN THE PRESENCE OF  HYDRATED C60 FULLERENE NANOSTRUCTURES."

А.О. Тихомиров, Д.Б. Шахнін, О.В.Тронза, С.C. Кошелєва, Г.В. Андрієвський.

ПРИСКОРЕННЯ ЛІЗИСУ ФІБРИНОВИХ ЗГУСТКІВ У ПРИСУТНОСТІ ГІДРАТОВАНИХ НАНОЧАСТОК ФУЛЕРЕНУ С60. Медична Хімія, червень 2008.

The English abstract is cited below.

What's the significance of this discovery? Good news for people suffering with the silent killer...a cure & a potential preventive action against blood clots or deep vein thrombosis (DVT).

ACCELERATION OF FIBRIN CLOT LYSIS IN THE PRESENCE OF HYDRATED NANO-PARTICLES OF FULLERENE C₆₀

  

A.O. Tykhomyrov¹, D.B. Shakhnin², O.V. Tronza³, S.S. Kosheleva¹,  G.V. Andrievsky⁴

  

1 – DNIEPROPETROVSK NATIONAL UNIVERSITY

2 – PUBLIC INTERNATIONAL UNIVERSITY OF HUMAN DEVELOPMENT “UKRAINE”, KYIV

3 – PALLADIN INSTITUTE OF BIOCHEMISTRY, KYIV

4 – STC “INSTITUTE FOR MONOCRYSTALS”, KHARKIV

Summary

    Effect of hydrated fullerene C₆₀ (C₆₀HyFn) onto kinetics parameters of enzymatic hydrolysis of fibrin clot induced by tissue plasminogen activator (t-PA) in vitro was studied. Incubation of t-PA in the C₆₀HyFn solution increased rate of clot lysis by 2,7 times and reduced time of half-lysis by 1,6 times. Data obtained suggest that enzyme fibrinolytic activity elevation occurs due to stabilization of enzyme water microenvironment in the presence of C₆₀HyFn. Application of fullerene C₆₀ may be useful for creation of highly efficient thrombolytical drugs.

KEY WORDS: fibrinolysis, tissue plasminogen activator, fullerene.

An English version of the research has been accepted for publication in a prestigious nanotechnology publication and is due to come out Oct 2010.

THE ACCELERATION OF BLOOD PLASMA CLOT LYSIS IN THE PRESENCE OF HYDRATED C60 FULLERENE NANOSTRUCTURES IN SUPER-SMALL CONCENTRATION by G. Andrievsky, D. Shakhnin, A. Tronza, D. Zhernosekov, A. Tykhomyrov.  Fullerenes, Nanotubes and Carbon Nanostructures, Oct 26, 2010.  DOI: 10.1080/15363831003785257.

Walter Derzko, The Opportunity Clinic, Smart Economy, Toronto