Showing posts with label Microbiology. Show all posts
Showing posts with label Microbiology. Show all posts

Daily Science Journal (Feb. 13, 2008) — If humans had see-through skin like a jellyfish, spotting disease like cancer would be a snap: Just look, and see a tumor form or grow.

Diagram of chicken breast tissue (approximately 250 microns thick) with photo-refractive crystal to counteract the scattering of light and remove the distortion it creates in images. The lower diagram would show the clearest image. (Credit: Caltech Biophotonics Laboratory)

But humans, of course, are not remotely diaphanous. "The reason a person is not transparent is that their tissues are highly scattering," sending light waves careening through the tissue instead of straight through, as they would through the tissue of that jellyfish, explains Changhuei Yang of the California Institute of Technology.

This scattering, in addition to rendering all of us opaque, makes the detection of disease a much trickier issue, requiring a host of diagnostic tests and procedures. But not, perhaps, for much longer, thanks to a new optical trick developed by Yang, an assistant professor of electrical engineering and bioengineering, and his colleagues, that counteracts the scattering of light and removes the distortion it creates in images.


It is well known that light scattering in a material is not exactly the random and unpredictable process one might imagine. In fact, scattering is deterministic, which means that the path that a beam of light takes as it traverses a particular slice of tissue and bounces and rebounds off of individual cells, is entirely predictable; if you again bounce light through that same swath of cells, it will scatter in exactly the same way.

The process is even reversible; if the individual photons of light that scattered through the tissue could be collected and sent back through the tissue, they'd bounce back along the same path and converge at the original spot from which they were sent. "The process is similar to the scattering of billiard balls on a pool table. If you can precisely reverse the paths and velocities of the billiard balls, you can cause the billiard balls to reassemble themselves into a rack," Yang explains.

Yang, along with his colleagues at Caltech, École Polytechnique Fédérale de Lausanne in Switzerland, and MIT, exploited this phenomenon to offset the murky nature of our tissues.

Their technique, called turbidity suppression by optical phase conjugation (TSOPC), is surprisingly simple. The scientists used a holographic crystal to record the scattered light pattern emerging from a 0.46-mm-thick piece of chicken breast. They then holographically played the pattern back through the tissue section to recover the original light beam. "This is similar to grabbing hold of the direction of time flow and turning it around; the time-reversed photons must retrace their trajectories through the tissue," Yang says. "The task is formidable though, as this is comparable to starting with a rack of 10 to the 18th power billiard balls (or photons), scattering them around the table, and attempting to reassemble them into a rack."

"Until we did this study, it wasn't clear that the effect will be observable with biological tissues. We were pleasantly surprised that the effect was readily observable and remarkably robust," Yang says. "This study opens up numerous possibilities in the use of optical time reversal in biomedicine."

One possible use of the technique is in photodynamic therapy, in which a highly focused beam of light is aimed at cancerous cells that have absorbed cell-killing light-sensitive compounds. When the light hits the cells, the compounds are activated and destroy the cells. Photodynamic therapy is most effective in treating cancers on the skin surface. Yang's technique, however, offers a way to concentrate light onto cancer-killing compounds located more deeply within tissue.

Yang's idea is to inject strongly light-scattering particles that are coated with light-activated cancer-killing drugs into diseased tissue. Shine a beam of light into the tissue, and it would be reflected off the scattering compounds as it bounces through the tissue. Some of the scattered light would return to the source, where it could be recorded as a hologram.

This hologram would contain information about the path that the scattered light took through the tissue, and, in effect, describe the optimal path BACK toward the light-scattering molecule--and the cancer-killing compounds. Playing back the signal with a stronger burst of light will then activate the therapeutic drugs, which kill the cancer cells.

In addition, the technique could offer a way to power miniature implants buried deep within tissues. "If you take a quick survey of what is out there at present, you will see that implants are fairly large," Yang says. "For example, a pacemaker is about the size of a cell phone. Why are they so big? A large part of the reason is because they need to carry their own power sources."

The key to making smaller implants, then--say, the size of a pen tip--is to eliminate the power sources. "I think implants that carry photovoltaic receivers are particularly promising," he says. "The effect can be applied to tailor light-delivery mechanisms to efficiently channel light into tissues and onto these implants."

A study describing the process appears in the February issue of the journal Nature Photonics. Zahid Yaqoob, a postdoctoral fellow in electrical engineering at Caltech, performed most of the experiments reported in the paper. The other authors of the paper are Demetri Psaltis, professor of optics and dean of engineering, École Polytechnique Fédérale de Lausanne in Switzerland, and Michael S. Feld, a professor of physics at MIT.

Adapted from materials provided by California Institute of Technology.



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Daily Science Journal (Feb. 10, 2008) — An international clinical trial has found that acyclovir, a common medication for treating herpes simplex virus-2 (HSV-2), the most common cause of genital herpes, does not reduce the risk of HIV infection when taken by people infected with HSV-2. Multiple studies have shown that people with HSV-2 have a higher risk of acquiring HIV. Researchers had hoped that acyclovir's ability to suppress the herpes virus, and its associated genital sores and breaks in the skin, could cut down on the likelihood of HIV being transmitted to a person with HSV-2 during sexual intercourse.

The Phase III clinical trial was led by the University of Washington in Seattle, in coordination with the HIV Prevention Trials Network, an international consortium funded by the National Institute of Allergy and Infectious Diseases (NIAID) in the National Institutes of Health. The findings were presented this week at the Conference on Retroviruses and Opportunistic Infections in Boston.


"The study was successful in answering the question of whether acyclovir could cut down on the risk of HIV acquisition for people infected with HSV-2," explained Dr. Connie Celum, the leader of the study and a UW professor of global health and medicine in the Division of Allergy and Infectious Disease and director of the International Clinical Research Center in the UW Department of Global Health. "We were hopeful that acyclovir would help reduce HIV acquisition in people with HSV-2. Though the study did not find that acyclovir helped with HIV acquisition, we did find that it reduced genital ulcers associated with HSV-2. Now we need to continue our research on the mechanisms through which HSV-2 acts as a risk factor for HIV, and how we might be able to use that knowledge to reduce the spread of HIV."

HSV-2 is one of the most common sexually transmitted infections worldwide and is especially prevalent in areas with high rates of HIV infection. Most people who are infected with HSV-2 do not know they have the virus because symptoms can be mild or absent. In some infected individuals, the virus can produce recurring genital herpes, a condition characterized by sores and breaks in the skin of the genital region. An active HSV-2 infection also attracts immune-system cells called CD-4 T-cells to the genital region, and HIV easily attaches to this type of cell. Multiple studies have shown that people with HSV-2 have a two-fold increase in their risk of acquiring HIV.

This study followed up on those results to test the theory that suppressing HSV-2 could cut down on HIV acquisition. It was launched in 2003, and with nine study sites in Peru, South Africa, Zambia, Zimbabwe, and the United States, it was the largest study yet of herpes suppression. There were 3,277 people with HSV-2 initially enrolled in the study, 105 people excluded, and 3,172 people included in the final analysis. Volunteers in Peru and the United States were HSV-2-infected men who have sex with men, and volunteers in Africa were HSV-2-infected women.

Half of the participants were randomly assigned to receive either a placebo or a standard daily dose of acyclovir, 400 mg twice a day. The study was double-blinded, meaning that neither participants nor care providers knew which treatment the participants were receiving. Both the placebo and treatment groups received standard HIV-prevention treatment, which includes being supplied with condoms and given extensive counseling on how to reduce the risk of HIV infection.

Researchers found that there was a 3.9 percent HIV incidence rate, a total of 75 cases, in participants who received acyclovir suppression, and a 3.3 percent HIV incidence rate, or 64 cases, in the placebo group. The difference between the groups was not statistically significant. The acyclovir treatment did succeed in reducing genital ulcers -- participants in the treatment group had a 37 percent reduction in genital ulcer incidence, and a significantly lower proportion of ulcers due to HSV-2.

"The study answered the scientific questions it was designed to answer," says Dr. Anna Wald, a UW professor of medicine and epidemiology who also helped lead the study. "The sites were able to recruit and retain a large number of volunteers, who maintained a high level of adherence to the twice-daily drug regimen. While we are disappointed with the results, the study was well-conducted and provides a clear answer about using acyclovir to reduce the risk of becoming HIV-infected."

The study participants have been informed of the findings and are being counseled on the continued need to avoid HIV exposure. Volunteers who became infected with HIV during the trial have been referred for appropriate medical care and treatment.

The study was supported by NIAID, and the acyclovir was supplied by GlaxoSmithKline. The HIV Prevention Trials Network is led by Family Health International, the network laboratory of Johns Hopkins University, and the Statistical Center for HIV/AIDS Research and Prevention at the Fred Hutchinson Cancer Research Center in Seattle. The study was conducted at the following sites: Iquitos, Lima and Pucallpa, in Peru; Johannesburg, South Africa; New York, San Francisco, and Seattle, in the United States; Lusaka, Zambia; and Harare, Zimbabwe.

Adapted from materials provided by University Of Washington.



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Daily Science Journal (Feb. 4, 2008) — DNA is the blueprint of all life, giving instruction and function to organisms ranging from simple one-celled bacteria to complex human beings. Now Northwestern University researchers report they have used DNA as the blueprint, contractor and construction worker to build a three-dimensional structure out of gold, a lifeless material.

Computer rendition of a structure created by using DNA to assemble nanoparticles into well-defined crystal lattices. (Credit: Northwestern University)

Using just one kind of nanoparticle (gold) the researchers built two common but very different crystalline structures by merely changing one thing -- the strands of synthesized DNA attached to the tiny gold spheres. A different DNA sequence in the strand resulted in the formation of a different crystal.

The technique, to be published in the journal Nature, and reflecting more than a decade of work, is a major and fundamental step toward building functional "designer" materials using programmable self-assembly. This "bottom-up" approach will allow scientists to take inorganic materials and build structures with specific properties for a given application, such as therapeutics, biodiagnostics, optics, electronics or catalysis


Most gems, such as diamonds, rubies and sapphires, are crystalline inorganic materials. Within each crystal structure, the atoms have precise locations, which give each material its unique properties. Diamond's renowned hardness and refractive properties are due to its structure -- the precise location of its carbon atoms.

In the Northwestern study, gold nanoparticles take the place of atoms. The novel part of the work is that the researchers use DNA to drive the assembly of the crystal. Changing the DNA strand's sequence of As, Ts, Gs and Cs changes the blueprint, and thus the shape, of the crystalline structure. The two crystals reported in Nature, both made of gold, have different properties because the particles are arranged differently.

"We are now closer to the dream of learning, as nanoscientists, how to break everything down into fundamental building blocks, which for us are nanoparticles, and reassembling them into whatever structure we want that gives us the properties needed for certain applications," said Chad A. Mirkin, one of the paper's senior authors and George B. Rathmann Professor of Chemistry in the Weinberg College of Arts and Sciences, professor of medicine and professor of materials science and engineering. In addition to Mirkin, George C. Schatz, Morrison Professor of Chemistry, directed the work.

By changing the type of DNA on the surface of the particles, the Northwestern team can get the particles to arrange differently in space. The structures that finally form are the ones that maximize DNA hybridization. DNA is the stabilizing force, the glue that holds the structure together. "These structures are a new form of matter," said Mirkin, "that would be difficult, if not impossible, to make any other way."

He likens the process to building a house. Starting with basic materials such as bricks, wood, siding, stone and shingles, a construction team can build many different types of houses out of the same building blocks. In the Northwestern work, the DNA controls where the building blocks (the gold nanoparticles) are positioned in the final crystal structure, arranging the particles in a functional way. The DNA does all the heavy lifting so the researchers don't have to.

Mirkin, Schatz and their team just used one building block, gold spheres, but as the method is further developed, a multitude of building blocks of different sizes can be used -- with different composition (gold, silver and fluorescent particles, for example) and different shapes (spheres, rods, cubes and triangles). Controlling the distance between the nanoparticles is also key to the structure's function.

"Once you get good at this you can build anything you want," said Mirkin, director of Northwestern's International Institute for Nanotechnology.

"The rules that govern self-assembly are not known, however," said Schatz, "and determining how to combine nanoparticles into interesting structures is one of the big challenges of the field."

The Northwestern researchers started with gold nanoparticles (15 nanometers in diameter) and attached double-stranded DNA to each particle with one of the strands significantly longer than the other. The single-stranded portion of this DNA serves as the "linker DNA," which seeks out a complementary single strand of DNA attached to another gold nanoparticle. The binding of the two single strands of linker DNA to each other completes the double helix, tightly binding the particles to each other.

Each gold nanoparticle has multiple strands of DNA attached to its surface so the nanoparticle is binding in many directions, resulting in a three-dimensional structure -- a crystal. One sequence of linker DNA, programmed by the researchers, results in one type of crystal structure while a different sequence of linker DNA results in a different structure.

"We even found a case where the same linker could give different structures, depending on the temperatures at which the particles were mixed," said Schatz.

Using the extremely brilliant X-rays produced by the Advanced Photon Source synchrotron at Argonne National Laboratory in combination with computational simulations, the research team imaged the crystals to determine the exact location of the particles throughout the structure. The final crystals have approximately 1 million nanoparticles.

"It took scientists decades of work to learn how to synthesize DNA," said Mirkin. "Now we've learned how to use the synthesized form outside the body to arrange lifeless matter into things that are useful, which is really quite spectacular."

The Nature paper, entitled "DNA-programmable nanoparticle crystallization" is to be published January 31, 2008. In addition to Mirkin and Schatz, other authors are Sung Yong Park, a former postdoctoral fellow in Schatz's lab and now at the University of Rochester (lead author); graduate student Abigail K. R. Lytton-Jean, Northwestern University; Byeongdu Lee, Advanced Photon Source, Argonne National Laboratory; and Steven Weigand, Northwestern's DND-CAT Synchrotron Research Center at Argonne's Advanced Photon Source.

Adapted from materials provided by Northwestern University, via EurekAlert!, a service of AAAS.



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Daily Science Journal (Nov. 12, 2007) — Scientists from the Max Planck Institute for Infection Biology in Berlin discovered why lung, but not skin, anthrax infections are lethal. As reported in the newest issue of PloS Pathogen (November 2007) Neutrophils, a form of white blood cells, play a key role in anthrax infections.

A human neutrophil takes up Bacillus anthracis. (Image: MPI for Infection Biology)

They can kill Bacillus anthracis by producing a protein called alpha-defensin. This discovery might now pave the way towards the development of new therapiesfor the fatal lung form of anthrax.


Bacillus anthracis is the causative agent of anthrax. What makes Bacillus anthracis especially dangerous is that these bacteria can form spores. The spores are extremely resistant against environmental stress and can survive for years.Infection with Bacillus anthracis can take place either via the lung or through the skin. Interestingly, the lung form of anthrax is almost always fatal, whereas skin infections remain localized and are rarely lethal. In contrast to the lung form, the skin form of anthrax can be treated without problems and most patients recover. During the past few years, Bacillus anthracis has also been used as a weapon for bioterrorism. Anthrax spores were sent in envelopes and inhaled and resulted in the death of 5 people in the USA.

The findings of the lab of Arturo Zychlinsky now help clarifying why the skin form is harmless in contrast to the lung form. After a skin infection with Bacillus anthracis, neutrophils are recruited to the site of infection. Neutrophils are white blood cells that can identify and kill microbes. In the skin, neutrophils take up the spores, which germinate inside the neutrophil to a vegetative ("growing") bacterium. This vegetative bacterium is then attacked and killed within the neutrophil. The scientists succeeded in identifying the substance responsible for the killing of the bacteria. After fractionation of neutrophil components only one protein remained which is sufficient for killing Bacillus anthracis: alpha-defensin

This mechanism is not effective in the lung form of anthrax. Here, the number of neutrophils recruited to the site of infection is known to be low, and insufficient to kill bacteria. Thus, inhaled spores can germinate and spread through the organism. The scientists in Berlin now hope that their discovery will help to develop new drugs against the lung form of anthrax. There might be the possibility that the inhalation of alphadefensin might kill vegetative bacteria in the lung and prevent dissemination.

Adapted from materials provided by Max Planck Society.




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Daily Science Journal (Jul. 23, 2007) — Scientists have identified a chemical that could be used as a new drug against anthrax.

Anthrax is a deadly disease caused by spores that germinate into bacteria, which then release a deadly toxin. Spores that are inhaled by animals or people germinate in the lungs to form bacteria, which then spread throughout the body, releasing the toxin and triggering the disease. Since spore germination is needed to cause infection, preventing germination is a potentially efficient way to stop the infection.


Jurgen Brojatsch, Ernesto Abel-Santos, and colleagues identified seven chemicals that block the germination of cultured anthrax spores. They also showed that one of these compounds, 6-thioguanosine, blocked the spores' germination inside mammalian cells, thus blocking anthrax infection. The scientists are now planning to test 6-thioguanosine in mice infected with the anthrax bacterium. This compound is a known anticancer agent with well-studied pharmacological properties, which could help save time and money if it is used in clinical trials.

Article: "Identification of an in Vivo Inhibitor of Bacillus anthracis Spore Germination" by Monique Akoachere, Raynal C. Squires, Adel M. Nour, Ludmyl Angelov, Jurgen Brojatsch, and Ernesto Abel-Santos

Adapted from materials provided by American Society for Biochemistry and Molecular Biology, via EurekAlert!, a service of AAAS.




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