Research Roundup

• Miniaturized Lab Permits Saliva Screening on the Go
• Nano-Sized Probes Allow Researchers to See Tumors
• Defining Who We Are When We Work Together
• Enzyme Shown to Help Protect Genomic Stability

Miniaturized Lab Permits Saliva Screening on the Go

A team of scientists and engineers led by Dr. Daniel Malamud, professor of Biochemistry at the School of Dental Medicine, has developed a robust means of analyzing oral samples. They believe their work will lead to a kit, not much bigger than a credit card, which could detect exposure to a variety of substances, from narcotics to anthrax to common bacteria and viruses. Their plan would increase ease of detection and accelerate response time whether it was used in the middle of a public health incident or in a busy doctor office.

At the Annual Meeting of the American Association for the Advancement of Science, Dr. Malamud presented their work on creating a prototype oral swab kit that detects HIV and Bacillus cereus, a bacterium closely related to B. anthraci.

Research has shown that fluids in the mouth contain ions, drugs, bacteria, viruses, hormones, antibodies, growth factors, DNA and RNA. While some rapid saliva tests are already in use, such as alcohol and drug tests that can be performed on the spot by police, to replicate other tests, such as the presence of anthrax, would require an entire laboratory. Dr. Malamud and his colleagues are striving to, in essence, reproduce a laboratory in a small device that could be used in any setting and that would produce results in less than an hour.

One particular breakthrough was made by the laboratory of Dr. Haim Bau, professor in MEAM in SEAS in miniaturizing PCR, the technique of amplifying trace amounts of DNA or RNA to detectable levels.  

“Normally, PCR involves a thermocycler device about the size of a toaster oven that heat and cools a sample through a series of reactions,” Dr. Malamud said. “Bau and his wizards were able to duplicate the entire process in a loop just a few centimeters long that carries out the process in a fraction of the time.”

In the device that Dr. Malamud and his colleagues are working on to detect HIV or B. cereus, a sample is taken with a small sponge. The user than would insert the swab into a small device to squeeze out the contents of the sponge. The liquid could then be analyzed through a series of reactions that could determine the presence of antibodies, antigens, RNA or DNA that correspond to bacteria or viruses.

“Such a system could make a difference when tests are needed on the scene,” Dr. Malamud said. “This might be obviously necessary when it comes to a potential bioterrorism incident or an accident of exposure, but it could also make the difference in the doctor office or emergency room, when you would need to know whether or not to administer antibiotics.”

Nano-Sized Probes Allow Researchers to See Tumors

Nano-sized particles embedded with bright, light-emitting molecules have enabled researchers to visualize a tumor more than one centimeter below the skin surface using only infrared light. A team of chemists, bioengineers and medical researchers based at Penn and the University of Minnesota has lodged fluorescent materials called porphyrins within the surface of a polymersome, a cell-like vesicle, to image a tumor within a living rodent. Their findings, which represent a proof of principle for the use of emissive polymersomes to target and visualize tumors, appear in the February 7 online early edition of the Proceedings of the National Academy of Science.

“We have shown that the dispersion of thousands of brightly emissive multi-porphyrin fluorophores within the polymersome membrane can be used to optically image tissue structures deep below the skin—with the potential to go even deeper,” said Dr. Michael J. Therien, professor of chemistry at Penn.

This work takes advantage of years of effort in Dr. Therien laboratory focused on the design of highly fluorescent compounds. Polymersomes, which were developed by Penn professors Dr. Daniel A. Hammer, professor and chair of bioengineering and professor of chemical engineering, and Dr. Dennis Discher, associate professor of chemical biomolecular and bio-engineering and IME, in the mid-1990s, function much like the bilayered membranes of living cells. Whereas cell membranes are created from a double layer of fatty phospholipid chains, a polymersome is comprised of two layers of synthetic co-polymers. Like a living cell, the polymersome membrane has a hydrophobic core. The study shows that the fluorophores evenly disperse within this core, giving rise to a nanometer-sized light-emitting structure.

In their study, the researchers demonstrate how they can use these emissive polymersomes to target markers on the surface of a specific type of tumor cell. When exposed to near-infrared light, which can travel through tissue, the fluorophores within the polymersome respond with a bright near-infrared signal that can then be detected.

According to Dr. Therien, there is keen interest in developing new technology that will enable optical imaging of cancer tissue, as such technology will be less costly and more accessible than MRI-based methods and free of the harmful side effects associated with radioactivity. In this imaging system, the flourophores can also be tuned to respond to different wavelengths of near-infrared light. This sets the stage for using emissive polymersomes to target multiple cancer cell-surface markers in the body simultaneously.

Emissive polymersomes perform much like in vivo imaging systems that use semiconductor-based “quantum dots.” These quantum dots, however, are hard matter, which could collect within the circulatory system, potentially causing a stroke. According to the Penn researchers, brightly emissive polymersomes define the first nanotech optical imaging platform based on non-aggregating “soft matter” (polymers and porphyrins) and hence have enormous potential in biomedicine.

Defining Who We Are When We Work Together

Whether it is barn-raising or crafting a business plan, humans are among the few creatures that are able to work well cooperatively. According to Dr. Robert Kurzban, an evolutionary psychologist at Penn, our success in cooperation results from three distinct personality types.

“In any given group of people, you’ll find three kinds of people: Cooperators, Free Riders, and what we call Reciprocators. Cooperators do the most work and Free Riders do as little as possible, but most of us are Reciprocators. We hold back a bit to determine the chances of success before devoting our full energy to a project,” said Dr. Robert Kurzban, an assistant professor in the department of psychology. “We found that these traits remained fairly stable among people, and you could reliably predict how a group might perform if you know the percentage of each type of person in that group.”

Dr. Kurzban and Dr. Daniel Houser of George Mason University present their findings in the January 21 online early edition of the Proceedings of the National Academy of Sciences. The researchers used a computer-based experiment to assess the range of cooperative behaviors among people. While they cannot offer a complete explanation of how these traits might have evolved, they point to reciprocity as an important motive in human social behavior. According to Dr. Kurzban, it could also provide a simple lesson on the power of internal communications to managers and group leaders.

More than 80 subjects participated in the experiment in which they were given 50 tokens that they could choose to keep or place in a group pool. Tokens placed in the group pool doubled in value and, at the end of the time period, were distributed equally among members. About 17 percent of the participants could be classified as Cooperators, taking the most risk almost immediately. Free Riders, who prefer not to cooperate, made up 20 percent.

Enzyme Shown to Help Protect Genomic Stability

Genomes throughout the animal kingdom and beyond are characterized by extensive segments that are inactive, lengthy stretches of DNA containing multiple genes that are closed to gene transcription. Scientists believe one reason for this broad gene silencing is the vital need for genomic stability, for protection against unwanted recombinations of genetic material or other disruptions of the genome’s integrity.

Genomic instability, particularly in the regions at the ends of the chromosomes known as telomeres, has been linked to aging in humans and an elevated risk for aging-related diseases, the most prominent of which is cancer. For this reason, insights into the mechanisms of gene silencing could provide important guideposts for new approaches to retarding aging or treating cancer.

Now, an investigation led by researchers at The Wistar Institute has shown that an enzyme known as Ubp10 plays a vital role in protecting the telomeric regions of the genome from potential destabilizing molecular events. The enzyme helps to keep the genome structurally closed, unavailable for transcription and possibly protected from dangerous genetic recombinations with other regions of the genome. A report on the research, appeared in the February 18 issue of Molecular Cell.

“There are regions of the genome that have to be inaccessible,” says Dr. Shelley L. Berger, the Hilary Koprowski Professor, in the gene expression and regulation program at Wistar and senior author on the study.

The Ubp10 enzyme acts on histones, molecules that have attracted increasing attention from scientists as they move beyond sequencing the human genome to trying to better understand how DNA is managed and its activity regulated. Histones are small proteins around which DNA is coiled to create structures called nucleosomes. Compact strings of nucleosomes, then, form into chromatin, the substructure of chromosomes. In many cases, when the DNA is tightly wrapped around the histones, the genes cannot be accessed and their expression is repressed. When the coils of DNA around the histones are loosened or the histone molecules are altered, the genes become available for expression.

It is the complex activity governing this process to which Ubp10 contributes. Enzymatic modifications to histones control DNA activation or silencing through the addition or removal of acetyl, methyl, and ubiquitin molecules in prescribed sequences and patterns.

Ubp10 appears to work similarly and in concert with another enzyme called Sir2, which removes acetyl molecules from histones. Sir2 has also been associated with promoting genomic stability, and some studies have linked it intriguingly to the aging process. Some studies, have suggested that low-calorie diets that extend life also boost Sir2 activity dramatically.